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

Example 6 with TreeParser

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

the class BEASTTestCase method getTree.

public static Tree getTree(Alignment data, String tree) throws Exception {
    TreeParser t = new TreeParser();
    t.initByName("taxa", data, "newick", tree, "IsLabelledNewick", true);
    return t;
}

Example 7 with TreeParser

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

the class ExchangeOperatorTest method testNarrowExchange.

void testNarrowExchange(String sourceTree, String targetTree, int runs, Alignment data) throws Exception {
    // first test going from source to target
    double match = 0;
    for (int i = 0; i < runs; i++) {
        TreeParser tree = new TreeParser();
        tree.initByName("taxa", data, "newick", sourceTree, "IsLabelledNewick", true);
        State state = new State();
        state.initByName("stateNode", tree);
        state.initialise();
        Exchange operator = new Exchange();
        operator.initByName("isNarrow", true, "tree", tree, "weight", 1.0);
        double logHR = operator.proposal();
        String treeString = tree.getRoot().toNewick();
        if (treeString.equals(targetTree) && !Double.isInfinite(logHR)) {
            // proportion of accepts equals min(HR, 1.0)
            match += Math.min(Math.exp(logHR), 1.0);
        }
    }
    System.out.println(" Matches: " + match * 100.0 / runs + "%");
    // now test going from target to source
    double match2 = 0;
    for (int i = 0; i < runs; i++) {
        TreeParser tree = new TreeParser();
        tree.initByName("taxa", data, "newick", targetTree, "IsLabelledNewick", true);
        State state = new State();
        state.initByName("stateNode", tree);
        state.initialise();
        Exchange operator = new Exchange();
        operator.initByName("isNarrow", true, "tree", tree, "weight", 1.0);
        double logHR = operator.proposal();
        String treeString = tree.getRoot().toNewick();
        if (treeString.equals(sourceTree) && !Double.isInfinite(logHR)) {
            // proportion of accepts equals min(HR, 1.0)
            match2 += Math.min(Math.exp(logHR), 1.0);
        }
    }
    System.out.println(" Matches: " + match2 * 100.0 / runs + "%");
    assertTrue("difference(" + 100 * (match - match2) / runs + ") exceeds 1.0%", 100.0 * Math.abs(match - match2) / runs < 1.0);
}

Example 8 with TreeParser

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

the class ScaleOperatorTest method testTreeScaling.

@Test
public void testTreeScaling() {
    String newick = "((0:1.0,1:1.0)4:1.0,(2:1.0,3:1.0)5:0.5)6:0.0;";
    TreeParser tree = new TreeParser(newick, false, false, false, 0);
    Node[] node = tree.getNodesAsArray();
    ScaleOperator operator = new ScaleOperator();
    operator.initByName("tree", tree, "weight", 1.0);
    operator.proposal();
    // leaf node
    node = tree.getNodesAsArray();
    assertEquals(0.0, node[0].getHeight(), EPSILON);
    assertEquals(0.0, node[1].getHeight(), EPSILON);
    // leaf node, not scaled
    assertEquals(0.5, node[2].getHeight(), EPSILON);
    assertEquals(0.5, node[3].getHeight(), EPSILON);
    // internal nodes, all scaled
    // first determine scale factor
    double scale = node[4].getHeight() / 1.0;
    assertEquals(1.0 * scale, node[4].getHeight(), EPSILON);
    assertEquals(1.5 * scale, node[5].getHeight(), EPSILON);
    assertEquals(2.0 * scale, node[6].getHeight(), EPSILON);
}

Example 9 with TreeParser

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

the class TreeAnnotatorTest method setUp.

@Before
public void setUp() throws Exception {
    final String[] treesString = new String[] { "((A:1,B:1):1,(C:1,D:1):1);", "(((A:1,B:1):1,C:2):2,D:3);", "((A:2,(B:1,C:1):1):2,D:3);" };
    final String[] treesSAString = new String[] { "((((0:0.5,1:1.0):1.0,2:2.0):1.0,3:0.0):2.0,4:4.0);", "((((0:1.0,2:1.5):1.0,1:2.5):0.5,3:0.0):2.0,4:4.0);", "(((0:0.5,2:1.0):1.0,1:2.0):3.0,(3:0.2,4:2.2):1.8);", "((((0:1.0,2:1.5):1.0,1:2.5):0.2,4:1.7):0.3,3:0.0):0.0;" };
    treeAnnotator = new TreeAnnotator();
    treeAnnotatorSA = new TreeAnnotator();
    trees = new Tree[treesString.length];
    for (int i = 0; i < trees.length; i++) {
        trees[i] = new TreeParser(treesString[i], false, false, true, 1);
    }
    treesSA = new Tree[treesSAString.length];
    for (int i = 0; i < treesSA.length; i++) {
        treesSA[i] = new TreeParser(treesSAString[i], false, false, false, 0);
    }
    cladeSystem = new CladeSystem();
    cladeSystemSA = new CladeSystem();
}

Example 10 with TreeParser

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

the class TreeAnnotatorTest method testNewickTargetTree.

@Test
public void testNewickTargetTree() throws Exception {
    // create target tree file in temp folder
    TreeParser tree = new TreeParser("((A,B),(C,D))");
    String tmpFolder = org.fest.util.Files.temporaryFolder().toString();
    File target = new File(tmpFolder + "/target.tree");
    PrintStream outfile = new PrintStream(target);
    tree.init(outfile);
    outfile.println();
    tree.log(0, outfile);
    outfile.println();
    tree.close(outfile);
    outfile.close();
    // create input tree set
    File source = new File(tmpFolder + "/source.trees");
    outfile = new PrintStream(source);
    for (String treeString : new String[] { "((A:1,B:1):1,(C:1,D:1):1);", "(((A:1,B:1):1,C:2):2,D:3);", "((A:2,(B:1,C:1):1):2,D:3);" }) {
        outfile.println(treeString);
    }
    ;
    outfile.close();
    File summary = new File(tmpFolder + "/summary.tree");
    // run tree annotator
    String[] args = new String[] { "-target", target.getPath(), source.getPath(), summary.getPath() };
    TreeAnnotator.main(args);
    // make sure we get output
    String summaryString = BeautiDoc.load(summary);
    System.out.println(summaryString);
}