Examples with DefaultTreeModel dr.evomodel.tree.DefaultTreeModel used on opensource projects

Example 41 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class StarTreeModelParser method parseXMLObject.

/**
 * @return a tree object based on the XML element it was passed.
 */
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Tree tree = (Tree) xo.getChild(Tree.class);
    StarTreeModel treeModel = new StarTreeModel(xo.getId(), tree);
    Logger.getLogger("dr.evomodel").info("Creating a star tree model, '" + xo.getId() + "'");
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject cxo = (XMLObject) xo.getChild(i);
            if (cxo.getName().equals(ROOT_HEIGHT)) {
                if (cxo.getRawChild(0) instanceof Reference) {
                    // treeModel.setRootHeightParameter((Parameter) cxo.getChild(Parameter.class));
                    throw new XMLParseException("Can not provide idref to a new root height parameter");
                } else {
                    ParameterParser.replaceParameter(cxo, treeModel.getRootHeightParameter());
                }
            } else if (cxo.getName().equals(SHARE_ROOT)) {
                DefaultTreeModel sharedRoot = (DefaultTreeModel) cxo.getChild(DefaultTreeModel.class);
                treeModel.setSharedRootHeightParameter(sharedRoot);
            } else if (cxo.getName().equals(LEAF_HEIGHT)) {
                String taxonName;
                if (cxo.hasAttribute(TAXON)) {
                    taxonName = cxo.getStringAttribute(TAXON);
                } else {
                    throw new XMLParseException("taxa element missing from leafHeight element in treeModel element");
                }
                int index = treeModel.getTaxonIndex(taxonName);
                if (index == -1) {
                    throw new XMLParseException("taxon " + taxonName + " not found for leafHeight element in treeModel element");
                }
                NodeRef node = treeModel.getExternalNode(index);
                ParameterParser.replaceParameter(cxo, treeModel.getLeafHeightParameter(node));
            // } else if (cxo.getName().equals(NODE_HEIGHTS)) {
            // 
            // boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
            // boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
            // boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
            // 
            // if (!rootNode && !internalNodes && !leafNodes) {
            // throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeHeights element");
            // }
            // 
            // ParameterParser.replaceParameter(cxo, treeModel.createNodeHeightsParameter(rootNode, internalNodes, leafNodes));
            // 
            // } else if (cxo.getName().equals(NODE_RATES)) {
            // 
            // boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
            // boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
            // boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
            // double[] initialValues = null;
            // 
            // if (cxo.hasAttribute(INITIAL_VALUE)) {
            // initialValues = cxo.getDoubleArrayAttribute(INITIAL_VALUE);
            // }
            // 
            // if (!rootNode && !internalNodes && !leafNodes) {
            // throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeRates element");
            // }
            // 
            // ParameterParser.replaceParameter(cxo, treeModel.createNodeRatesParameter(initialValues, rootNode, internalNodes, leafNodes));
            // 
            // } else if (cxo.getName().equals(NODE_TRAITS)) {
            // 
            // boolean rootNode = cxo.getAttribute(ROOT_NODE, false);
            // boolean internalNodes = cxo.getAttribute(INTERNAL_NODES, false);
            // boolean leafNodes = cxo.getAttribute(LEAF_NODES, false);
            // boolean fireTreeEvents = cxo.getAttribute(FIRE_TREE_EVENTS, false);
            // String name = cxo.getAttribute(NAME, "trait");
            // int dim = cxo.getAttribute(MULTIVARIATE_TRAIT, 1);
            // 
            // double[] initialValues = null;
            // if (cxo.hasAttribute(INITIAL_VALUE)) {
            // initialValues = cxo.getDoubleArrayAttribute(INITIAL_VALUE);
            // }
            // 
            // if (!rootNode && !internalNodes && !leafNodes) {
            // throw new XMLParseException("one or more of root, internal or leaf nodes must be selected for the nodeTraits element");
            // }
            // 
            // ParameterParser.replaceParameter(cxo, treeModel.createNodeTraitsParameter(name, dim, initialValues, rootNode, internalNodes, leafNodes, fireTreeEvents));
            } else if (cxo.getName().equals(LEAF_TRAIT)) {
                String name = cxo.getAttribute(NAME, "trait");
                String taxonName;
                if (cxo.hasAttribute(TAXON)) {
                    taxonName = cxo.getStringAttribute(TAXON);
                } else {
                    throw new XMLParseException("taxa element missing from leafTrait element in treeModel element");
                }
                int index = treeModel.getTaxonIndex(taxonName);
                if (index == -1) {
                    throw new XMLParseException("taxon '" + taxonName + "' not found for leafTrait element in treeModel element");
                }
                NodeRef node = treeModel.getExternalNode(index);
                Parameter parameter = treeModel.getNodeTraitParameter(node, name);
                if (parameter == null)
                    throw new XMLParseException("trait '" + name + "' not found for leafTrait (taxon, " + taxonName + ") element in treeModel element");
                ParameterParser.replaceParameter(cxo, parameter);
            } else {
                throw new XMLParseException("illegal child element in " + getParserName() + ": " + cxo.getName());
            }
        } else if (xo.getChild(i) instanceof Tree) {
        // do nothing - already handled
        } else {
            throw new XMLParseException("illegal child element in  " + getParserName() + ": " + xo.getChildName(i) + " " + xo.getChild(i));
        }
    }
    Logger.getLogger("dr.evomodel").info("  initial tree topology = " + TreeUtils.uniqueNewick(treeModel, treeModel.getRoot()));
    Logger.getLogger("dr.evomodel").info("  tree height = " + treeModel.getNodeHeight(treeModel.getRoot()));
    return treeModel;
}

Example 42 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class NNITest method testDoOperation.

/**
 * Test method for {@link SimpleMCMCOperator#doOperation()}.
 * @throws ImportException
 * @throws IOException
 */
public void testDoOperation() throws IOException, ImportException {
    // probability of picking B node is 1/(2n-4) = 1/6
    // probability of swapping it with C is 1/1
    // total = 1/6
    System.out.println("Test 1: Forward");
    String treeMatch = "((((A,C),B),D),E);";
    int count = 0;
    int reps = 100000;
    for (int i = 0; i < reps; i++) {
        TreeModel treeModel = new DefaultTreeModel("treeModel", tree5);
        NNI operator = new NNI(treeModel, 1);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 1.0 / 6.0);
    assertExpectation(1.0 / 6.0, p_1, reps);
}

Example 43 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class GibbsSubtreeSwapTestProblem method testDoOperation.

/**
 * Test method for {@link dr.evomodel.operators.GibbsSubtreeSwap}.
 * @throws ImportException
 * @throws IOException
 */
public void testDoOperation() throws IOException, ImportException {
    // assumes that the posterior is equal for all trees!!!
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/2
    // total = 1/14
    // probability of picking {D} node is 1/(2n-3) = 1/7
    // probability of picking {A,B} is 1/5
    // total = 1/35
    // total = 1/14 + 1/35 = 7/70 = 0.1
    // now we calculate the same for the backward proposal
    // this is needed for the Hastings ratio
    // probability of picking (A,B) node is 1/(2n-3) = 1/7
    // probability of swapping with D is 1/3
    // total = 1/21
    // probability of picking {D} node is 1/(2n-3) = 1/7
    // probability of picking {A,B} is 1/4
    // total = 1/28
    // total = 1/21 + 1/28 = 4/84 + 3/84 = 7/84 = 1/12
    System.out.println("Test 1: Forward");
    String treeMatch = "(((D,C),(A,B)),E);";
    int count = 0;
    int reps = 100000;
    for (int i = 0; i < reps; i++) {
        DefaultTreeModel treeModel = new DefaultTreeModel("treeModel", tree5);
        GibbsSubtreeSwap operator = new GibbsSubtreeSwap(treeModel, false, 1.0);
        double hr = operator.operate(null);
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            // System.out.println("Expected Hastings ratio = " + 5.0/6.0 + " in log = " + Math.log(5.0/6.0));
            // System.out.println("Obtained Hastings ratio = " + Math.exp(hr) + " in log = " + hr);
            TestCase.assertEquals(Math.log(5.0 / 6.0), hr, 0.00000001);
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 0.1);
    assertExpectation(0.1, p_1, reps);
}

Example 44 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class AncestralStateTreeLikelihoodTest method testJointLikelihood.

public void testJointLikelihood() {
    TreeModel treeModel = new DefaultTreeModel("treeModel", tree);
    Sequence[] sequence = new Sequence[3];
    sequence[0] = new Sequence(new Taxon("0"), "A");
    sequence[1] = new Sequence(new Taxon("1"), "C");
    sequence[2] = new Sequence(new Taxon("2"), "C");
    Taxa taxa = new Taxa();
    for (Sequence s : sequence) {
        taxa.addTaxon(s.getTaxon());
    }
    SimpleAlignment alignment = new SimpleAlignment();
    for (Sequence s : sequence) {
        alignment.addSequence(s);
    }
    Parameter mu = new Parameter.Default(1, 1.0);
    Parameter kappa = new Parameter.Default(1, 1.0);
    double[] pi = { 0.25, 0.25, 0.25, 0.25 };
    Parameter freqs = new Parameter.Default(pi);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    AncestralStateTreeLikelihood treeLikelihood = new AncestralStateTreeLikelihood(alignment, treeModel, new GammaSiteModel(hky), new StrictClockBranchRates(mu), false, true, Nucleotides.INSTANCE, "state", false, // useMap = true
    true, false);
    double logLike = treeLikelihood.getLogLikelihood();
    StringBuffer buffer = new StringBuffer();
    TreeUtils.newick(treeModel, treeModel.getRoot(), false, TreeUtils.BranchLengthType.LENGTHS_AS_TIME, null, null, new TreeTraitProvider[] { treeLikelihood }, null, buffer);
    System.out.println(buffer);
    System.out.println("t_CA(2) = " + t(false, 2.0));
    System.out.println("t_CC(1) = " + t(true, 1.0));
    double trueValue = 0.25 * t(false, 2.0) * Math.pow(t(true, 1.0), 3.0);
    assertEquals(logLike, Math.log(trueValue), 1e-6);
}

Example 45 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class MsatFullLikelihoodTest method setUpExample3.

private void setUpExample3() throws Exception {
    // taxa
    ArrayList<Taxon> taxonList3 = new ArrayList<Taxon>();
    Collections.addAll(taxonList3, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"), new Taxon("taxon4"), new Taxon("taxon5"), new Taxon("taxon6"), new Taxon("taxon7"));
    Taxa taxa3 = new Taxa(taxonList3);
    // msat datatype
    Microsatellite msat = new Microsatellite(1, 4);
    Patterns msatPatterns = new Patterns(msat, taxa3);
    // pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 3, 1, 2, 3, 0, 1 });
    // create tree
    NewickImporter importer = new NewickImporter("(((taxon1:0.3,taxon2:0.3):0.6,taxon3:0.9):0.9,((taxon4:0.5,taxon5:0.5):0.3,(taxon6:0.7,taxon7:0.7):0.1):1.0);");
    Tree tree = importer.importTree(null);
    // treeModel
    TreeModel treeModel = new DefaultTreeModel(tree);
    // msatsubstModel
    AsymmetricQuadraticModel aqm3 = new AsymmetricQuadraticModel(msat, null);
    // siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm3);
    // treeLikelihood
    treeLikelihood3 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
}