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

Example 6 with SimpleNode

use of dr.evolution.tree.SimpleNode 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));
}

Example 7 with SimpleNode

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

the class AlloppDiploidHistory method makesimpletree.

// for testing
private SimpleTree makesimpletree() {
    SimpleNode[] snodes = new SimpleNode[dhnodes.length];
    for (int n = 0; n < dhnodes.length; n++) {
        snodes[n] = new SimpleNode();
        // I use taxon==null to identify joined leg node when removing hybtips
        snodes[n].setTaxon(null);
    }
    makesimplesubtree(snodes, 0, dhnodes[rootn]);
    return new SimpleTree(snodes[dhnodes.length - 1]);
}

Example 8 with SimpleNode

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

the class SimpleNodeParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    SimpleNode node = new SimpleNode();
    Taxon taxon = null;
    if (xo.hasAttribute(HEIGHT)) {
        node.setHeight(xo.getDoubleAttribute(HEIGHT));
    }
    if (xo.hasAttribute(RATE)) {
        node.setRate(xo.getDoubleAttribute(RATE));
    }
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object child = xo.getChild(i);
        if (child instanceof dr.evolution.tree.SimpleNode) {
            node.addChild((dr.evolution.tree.SimpleNode) child);
        } else if (child instanceof Taxon) {
            taxon = (Taxon) child;
        } else if (child instanceof Date) {
            node.setAttribute("date", child);
        } else if (child instanceof Attribute) {
            Attribute attr = (Attribute) child;
            String name = attr.getAttributeName();
            Object value = attr.getAttributeValue();
            node.setAttribute(name, value);
        } else if (child instanceof Attribute[]) {
            Attribute[] attrs = (Attribute[]) child;
            for (int j = 0; j < attrs.length; j++) {
                String name = attrs[j].getAttributeName();
                Object value = attrs[j].getAttributeValue();
                node.setAttribute(name, value);
            }
        } else if (child instanceof XMLObject) {
            XMLObject xoc = (XMLObject) child;
            if (xoc.getName().equals(Attributable.ATTRIBUTE)) {
                node.setAttribute(xoc.getStringAttribute(Attributable.NAME), xoc.getAttribute(Attributable.VALUE));
            } else {
                throw new XMLParseException("Unrecognized element" + xoc.getName() + " found in node element!");
            }
        } else {
            throw new XMLParseException("Unrecognized element found in node element!");
        }
    }
    if (taxon != null) {
        node.setTaxon(taxon);
    }
    return node;
}