Examples with SimpleTree dr.evolution.tree.SimpleTree used on opensource projects

Example 1 with SimpleTree

use of dr.evolution.tree.SimpleTree in project beast-mcmc by beast-dev.

the class TestCalibratedYuleModel method calibration.

private Tree calibration(final TaxonList taxa, DemographicModel demoModel) throws Exception {
    dr.evolution.coalescent.CoalescentSimulator simulator = new dr.evolution.coalescent.CoalescentSimulator();
    DemographicFunction demoFunction = demoModel.getDemographicFunction();
    SimpleNode[] firstHalfNodes = new SimpleNode[taxa.getTaxonCount() / 2];
    SimpleNode[] secondHalfNodes = new SimpleNode[taxa.getTaxonCount() - taxa.getTaxonCount() / 2];
    for (int i = 0; i < firstHalfNodes.length; i++) {
        firstHalfNodes[i] = new SimpleNode();
        firstHalfNodes[i].setTaxon(taxa.getTaxon(i));
    }
    for (int i = 0; i < secondHalfNodes.length; i++) {
        secondHalfNodes[i] = new SimpleNode();
        secondHalfNodes[i].setTaxon(taxa.getTaxon(i + taxa.getTaxonCount() / 2));
    }
    SimpleNode firstHalfRootNode = simulator.simulateCoalescent(firstHalfNodes, demoFunction);
    SimpleNode[] restNodes = simulator.simulateCoalescent(secondHalfNodes, demoFunction, 0, firstHalfRootNode.getHeight());
    SimpleNode[] together = new SimpleNode[restNodes.length + 1];
    for (int i = 0; i < restNodes.length; i++) {
        together[i + 1] = restNodes[i];
    }
    together[0] = firstHalfRootNode;
    SimpleNode root = simulator.simulateCoalescent(together, demoFunction);
    Tree tree = new SimpleTree(root);
    return tree;
}

Example 2 with SimpleTree

use of dr.evolution.tree.SimpleTree in project beast-mcmc by beast-dev.

the class TraceCorrelationAssert method createPrimateTreeModel.

//************************** data ****************************
protected TreeModel createPrimateTreeModel() {
    SimpleNode[] nodes = new SimpleNode[10];
    for (int n = 0; n < 10; n++) {
        nodes[n] = new SimpleNode();
    }
    //        nodes[0].setHeight(0);
    // human
    nodes[0].setTaxon(taxa[0]);
    // chimp
    nodes[1].setTaxon(taxa[1]);
    // bonobo
    nodes[2].setTaxon(taxa[2]);
    nodes[3].setHeight(0.010772);
    nodes[3].addChild(nodes[1]);
    nodes[3].addChild(nodes[2]);
    nodes[4].setHeight(0.024003);
    nodes[4].addChild(nodes[0]);
    nodes[4].addChild(nodes[3]);
    // gorilla
    nodes[5].setTaxon(taxa[3]);
    nodes[6].setHeight(0.036038);
    nodes[6].addChild(nodes[4]);
    nodes[6].addChild(nodes[5]);
    // orangutan
    nodes[7].setTaxon(taxa[4]);
    nodes[8].setHeight(0.069125);
    nodes[8].addChild(nodes[6]);
    nodes[8].addChild(nodes[7]);
    // siamang
    nodes[9].setTaxon(taxa[5]);
    SimpleNode root = new SimpleNode();
    root.setHeight(0.099582);
    root.addChild(nodes[8]);
    root.addChild(nodes[9]);
    Tree tree = new SimpleTree(root);
    tree.setUnits(Units.Type.YEARS);
    //treeModel
    return new TreeModel(tree);
}

Example 3 with SimpleTree

use of dr.evolution.tree.SimpleTree in project beast-mcmc by beast-dev.

the class NormalizedSequenceLikelihoodTest method createSillyTreeModel.

protected TreeModel createSillyTreeModel(int numTaxa) {
    SimpleNode[] nodes = new SimpleNode[2 * numTaxa - 1];
    for (int n = 0; n < 2 * numTaxa - 1; n++) {
        nodes[n] = new SimpleNode();
    }
    nodes[0].setTaxon(taxa[0]);
    nodes[1].setTaxon(taxa[1]);
    nodes[2].setHeight(1);
    nodes[2].addChild(nodes[0]);
    nodes[2].addChild(nodes[1]);
    SimpleNode root = nodes[2];
    if (numTaxa == 3) {
        nodes[3].setTaxon(taxa[2]);
        nodes[4].setHeight(2);
        nodes[4].addChild(nodes[2]);
        nodes[4].addChild(nodes[3]);
        root = nodes[4];
    }
    Tree tree = new SimpleTree(root);
    tree.setUnits(Units.Type.YEARS);
    //treeModel
    return new TreeModel(tree);
}

Example 4 with SimpleTree

use of dr.evolution.tree.SimpleTree in project beast-mcmc by beast-dev.

the class SimpleTreeParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    boolean usingDates = xo.getAttribute(USING_DATES, false);
    SimpleNode root = (SimpleNode) xo.getChild(SimpleNode.class);
    if (root == null) {
        throw new XMLParseException("node element missing from tree");
    }
    SimpleTree tree = new SimpleTree(root);
    if (usingDates) {
        dr.evolution.util.Date mostRecent = null;
        for (int i = 0; i < tree.getTaxonCount(); i++) {
            dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getTaxonAttribute(i, DATE);
            if (date == null) {
                date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getExternalNode(i), DATE);
            }
            if (date != null && ((mostRecent == null) || date.after(mostRecent))) {
                mostRecent = date;
            }
        }
        for (int i = 0; i < tree.getInternalNodeCount(); i++) {
            dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getInternalNode(i), DATE);
            if (date != null && ((mostRecent == null) || date.after(mostRecent))) {
                mostRecent = date;
            }
        }
        if (mostRecent == null) {
            throw new XMLParseException("no date elements in tree (and usingDates attribute set)");
        }
        TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
        for (int i = 0; i < tree.getTaxonCount(); i++) {
            dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getTaxonAttribute(i, DATE);
            if (date == null) {
                date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getExternalNode(i), DATE);
            }
            if (date != null) {
                double height = timeScale.convertTime(date.getTimeValue(), date);
                tree.setNodeHeight(tree.getExternalNode(i), height);
            }
        }
        for (int i = 0; i < tree.getInternalNodeCount(); i++) {
            dr.evolution.util.Date date = (dr.evolution.util.Date) tree.getNodeAttribute(tree.getInternalNode(i), DATE);
            if (date != null) {
                double height = timeScale.convertTime(date.getTimeValue(), date);
                tree.setNodeHeight(tree.getInternalNode(i), height);
            }
        }
        MutableTree.Utils.correctHeightsForTips(tree);
    }
    tree.setUnits(units);
    return tree;
}

Example 5 with SimpleTree

use of dr.evolution.tree.SimpleTree in project beast-mcmc by beast-dev.

the class StructuredCoalescentSimulator method simulateTree.

/**
     * Simulates a coalescent tree, given a taxon list.
     *
     * @param taxa          the set of taxa to simulate a coalescent tree between
     * @param demoFunctions the demographic function to use
     */
public Tree simulateTree(TaxonList[] taxa, DemographicFunction[] demoFunctions, ColourChangeMatrix colourChangeMatrix) {
    SimpleNode[][] nodes = new SimpleNode[taxa.length][];
    for (int i = 0; i < taxa.length; i++) {
        nodes[i] = new SimpleNode[taxa[i].getTaxonCount()];
        for (int j = 0; j < taxa[i].getTaxonCount(); j++) {
            nodes[i][j] = new SimpleNode();
            nodes[i][j].setTaxon(taxa[i].getTaxon(j));
        }
    }
    dr.evolution.util.Date mostRecent = null;
    boolean usingDates = false;
    for (int i = 0; i < taxa.length; i++) {
        for (int j = 0; j < taxa[i].getTaxonCount(); j++) {
            if (TaxonList.Utils.hasAttribute(taxa[i], j, dr.evolution.util.Date.DATE)) {
                usingDates = true;
                dr.evolution.util.Date date = (dr.evolution.util.Date) taxa[i].getTaxonAttribute(j, dr.evolution.util.Date.DATE);
                if ((date != null) && (mostRecent == null || date.after(mostRecent))) {
                    mostRecent = date;
                }
            } else {
                // assume contemporaneous tips
                nodes[i][j].setHeight(0.0);
            }
        }
    }
    if (usingDates) {
        assert mostRecent != null;
        TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
        for (int i = 0; i < taxa.length; i++) {
            for (int j = 0; j < taxa[i].getTaxonCount(); j++) {
                dr.evolution.util.Date date = (dr.evolution.util.Date) taxa[i].getTaxonAttribute(j, dr.evolution.util.Date.DATE);
                if (date == null) {
                    throw new IllegalArgumentException("Taxon, " + taxa[i].getTaxonId(j) + ", is missing its date");
                }
                nodes[i][j].setHeight(timeScale.convertTime(date.getTimeValue(), date));
            }
            if (demoFunctions[0].getUnits() != mostRecent.getUnits()) {
            //throw new IllegalArgumentException("The units of the demographic model and the most recent date must match!");
            }
        }
    }
    return new SimpleTree(simulateCoalescent(nodes, demoFunctions, colourChangeMatrix));
}