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

Example 21 with TreeParser

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

the class MarginalTreeTest method testNonOverlapping.

@Test
public void testNonOverlapping() throws Exception {
    // Conversion graph
    String str = "[&locus,2,2759,0.3260126313706676,10,2808,0.42839862922656696] " + "[&locus,10,6692,0.3381366423491633,2,6693,0.5683827224649434] " + "[&locus,10,8069,0.2807615297583804,14,8160,0.3415740002783274] " + "[&locus,2,9000,0.1,2,9500,0.4] " + "[&locus,2,9530,0.2,18,9600,2.0] " + "(((0:0.04916909893812008,1:0.04916909893812008)10:0.5465237639426681," + "(4:0.3773111326866937,(((8:0.22180790639747835," + "(3:0.07561592852503513,6:0.07561592852503513)11:0.14619197787244323)" + "13:0.010206467073885589,9:0.23201437347136394)14:0.116542689187905," + "(7:0.10746702934931932,5:0.10746702934931932)12:0.24109003330994963)" + "15:0.02875407002742475)16:0.21838173019409446)17:1.1073878800617445," + "2:1.7030807429425328)18:0.0";
    Locus locus = new Locus("locus", 10000);
    locus.setID("locus");
    ConversionGraph acg = new ConversionGraph();
    acg.initByName("fromString", str, "locus", locus);
    // System.out.println(acg.getExtendedNewick(true));
    // Test all marginals against truth
    // (I have eyeballed each of these trees and claim that they are correct.)
    String[] correctNewickStrings = { "(((0:0.04916909893812016,1:0.04916909893812016)10:0.5465237639426681,(((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:0.21838173019409446)17:1.1073878800617445,2:1.7030807429425328)18:0.0", "((2:0.42839862922656696,(0:0.04916909893812016,1:0.04916909893812016)10:0.3792295302884468)18:0.1672942336542213,(((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:0.21838173019409446)17:0.0", "(((0:0.04916909893812016,1:0.04916909893812016)10:0.5465237639426681,(((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:0.21838173019409446)17:1.1073878800617445,2:1.7030807429425328)18:0.0", "((((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:1.325769610255839,((0:0.04916909893812016,1:0.04916909893812016)10:0.5192136235268232,2:0.5683827224649434)17:1.1346980204775894)18:0.0", "(((0:0.04916909893812016,1:0.04916909893812016)10:0.5465237639426681,(((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:0.21838173019409446)17:1.1073878800617445,2:1.7030807429425328)18:0.0", "(((((0:0.04916909893812016,1:0.04916909893812016)10:0.29240490134020725,(((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.1095596268069634)17:0.006983062380941707,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:1.325769610255839,2:1.7030807429425328)18:0.0", "(((0:0.04916909893812016,1:0.04916909893812016)10:0.5465237639426681,(((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:0.21838173019409446)17:1.1073878800617445,2:1.7030807429425328)18:0.0", "(((0:0.04916909893812016,1:0.04916909893812016)10:0.5465237639426681,(((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:0.21838173019409446)17:1.1073878800617445,2:1.7030807429425328)18:0.0", "(((0:0.04916909893812016,1:0.04916909893812016)10:0.5465237639426681,(((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:0.21838173019409446)17:1.1073878800617445,2:1.7030807429425328)18:0.0", "(((0:0.04916909893812016,1:0.04916909893812016)10:0.5465237639426681,(((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:0.21838173019409446)17:1.4043071371192117,2:2.0)18:0.0;", "(((0:0.04916909893812016,1:0.04916909893812016)10:0.5465237639426681,(((((3:0.07561592852503529,6:0.07561592852503529)11:0.1461919778724432,8:0.2218079063974785)13:0.010206467073885506,9:0.232014373471364)14:0.11654268918790511,(5:0.1074670293493194,7:0.1074670293493194)12:0.24109003330994971)15:0.028754070027424694,4:0.3773111326866938)16:0.21838173019409446)17:1.1073878800617445,2:1.7030807429425328)18:0.0" };
    for (int r = 0; r < acg.getRegionCount(locus); r++) {
        MarginalTree marginalTree = new MarginalTree(acg, acg.getRegions(locus).get(r));
        // System.out.println(marginalTree + ";");
        assertTrue(treesEquivalent(marginalTree.getRoot(), new TreeParser(correctNewickStrings[r], false, true, false, 0).getRoot(), 1e-15));
    }
}

Example 22 with TreeParser

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

the class ACGLikelihoodApproxTest method testTreeHeightMap.

@Test
public void testTreeHeightMap() throws Exception {
    List<Sequence> sequences = new ArrayList<>();
    // 01234567890123456789
    sequences.add(new Sequence("t1", "GGGGGGGGGGGGGGGGGGGG"));
    sequences.add(new Sequence("t2", "CCCCCCCCCCCCCCCCCCCC"));
    sequences.add(new Sequence("t3", "TTTTTTTTTTTTTTTTTTTT"));
    Alignment alignment = new Alignment(sequences, "nucleotide");
    Locus locus = new Locus("locus", alignment);
    TreeParser tree = new TreeParser(alignment, "((t1:1,t2:1):1,t3:2):0;");
    ConversionGraph acg = new ConversionGraph();
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    ACGLikelihoodApprox likelihoodApprox = new ACGLikelihoodApprox();
    likelihoodApprox.initByName("acg", acg, "substitutionRate", "1.0", "alignment", alignment, "locus", locus);
    Map<Double, Coalescence> heightMap = likelihoodApprox.getCoalescenceHeights();
    Assert.assertEquals(2, heightMap.size());
    Assert.assertTrue(heightMap.containsKey(1.0));
    Assert.assertTrue(heightMap.containsKey(2.0));
    Assert.assertTrue(heightMap.get(1.0).equals(new Coalescence("[0,20]{0}{1}")));
    Assert.assertTrue(heightMap.get(2.0).equals(new Coalescence("[0,20]{0,1}{2}")));
}

Example 23 with TreeParser

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

the class ConversionGraph method fromStringOld.

/**
 * Load ACG from old string representation.
 *
 * @param str string representation of ACG
 */
@Deprecated
public void fromStringOld(String str) {
    // Extract clonal frame and recombination components of string
    Pattern cfPattern = Pattern.compile("^[^\\(]*(\\(.*)$");
    Matcher cfMatcher = cfPattern.matcher(str);
    if (!cfMatcher.find())
        throw new RuntimeException("Error parsing ACG state string.");
    // Process clonal frame
    String sNewick = cfMatcher.group(cfMatcher.groupCount());
    try {
        TreeParser parser = new TreeParser();
        parser.thresholdInput.setValue(1e-10, parser);
        parser.offsetInput.setValue(0, parser);
        setRoot(parser.parseNewick(sNewick));
    } catch (Exception ex) {
        Logger.getLogger(ConversionGraph.class.getName()).log(Level.SEVERE, null, ex);
    }
    initArrays();
    Pattern convPattern = Pattern.compile("\\[&([^]]*)]");
    Matcher convMatcher = convPattern.matcher(str);
    // Process recombinations
    for (Locus locus : getLoci()) convs.get(locus).clear();
    while (convMatcher.find()) {
        String[] elements = convMatcher.group(1).split(",");
        Locus locus = getLocusByID(elements[0]);
        if (locus == null)
            throw new RuntimeException("Uknown locus id " + elements[0] + ".  Aborting.");
        Node node1 = getNode(Integer.parseInt(elements[1]));
        int startLocus = Integer.parseInt(elements[2]);
        double height1 = Double.parseDouble(elements[3]);
        Node node2 = getNode(Integer.parseInt(elements[4]));
        int endLocus = Integer.parseInt(elements[5]);
        double height2 = Double.parseDouble(elements[6]);
        Conversion conv = new Conversion(node1, height1, node2, height2, startLocus, endLocus, this, locus);
        addConversion(conv);
    }
    if (isInvalid()) {
        throw new IllegalArgumentException("Invalid ACG read from string. Aborting.");
    }
}

Example 24 with TreeParser

use of beast.util.TreeParser in project MultiTypeTree by tgvaughan.

the class MultiTypeTree method fromXML.

// ///////////////////////////////////////////////
// Serialization and deserialization for state //
// ///////////////////////////////////////////////
/**
 * reconstruct tree from XML fragment in the form of a DOM node *
 * @param node
 */
@Override
public void fromXML(org.w3c.dom.Node node) {
    try {
        String sNewick = node.getTextContent();
        TreeParser parser = new TreeParser();
        parser.initByName("IsLabelledNewick", false, "offset", 0, "adjustTipHeights", false, "singlechild", true, "newick", sNewick);
        // parser.m_nThreshold.setValue(1e-10, parser);
        // parser.m_nOffset.setValue(0, parser);
        initFromFlatTree(parser, true);
        initArrays();
    } catch (Exception ex) {
        Logger.getLogger(MultiTypeTree.class.getName()).log(Level.SEVERE, null, ex);
    }
}

Example 25 with TreeParser

use of beast.util.TreeParser in project MultiTypeTree by tgvaughan.

the class MultiTypeTreeFromNewick method initAndValidate.

@Override
public void initAndValidate() {
    super.initAndValidate();
    TreeParser parser = new TreeParser();
    parser.initByName("IsLabelledNewick", true, "adjustTipHeights", adjustTipHeightsInput.get(), "singlechild", true, "newick", newickStringInput.get());
    initFromFlatTree(parser, true);
}