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

Example 21 with Tree

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

the class TreeMetricStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeMetricStatistic.Method m = TreeMetricStatistic.Method.TOPOLOGY;
    if (xo.hasAttribute(METHOD)) {
        final String s = xo.getStringAttribute(METHOD);
        m = TreeMetricStatistic.Method.valueOf(s.toUpperCase());
    }
    final String name = xo.getAttribute(Statistic.NAME, xo.hasId() ? xo.getId() : m.name());
    final Tree target = (Tree) xo.getElementFirstChild(TARGET);
    final Tree reference = (Tree) xo.getElementFirstChild(REFERENCE);
    return new TreeMetricStatistic(name, target, reference, m);
}

Example 22 with Tree

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

the class NodeHeightsStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    Parameter groupSizes = (Parameter) xo.getChild(Parameter.class);
    return new NodeHeightsStatistic(name, tree, groupSizes);
}

Example 23 with Tree

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

the class ParsimonyStateStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    XMLObject cxo = xo.getChild(STATE);
    TaxonList stateTaxa = (TaxonList) cxo.getChild(TaxonList.class);
    cxo = xo.getChild(MRCA);
    TaxonList mrcaTaxa = (TaxonList) cxo.getChild(TaxonList.class);
    try {
        return new ParsimonyStateStatistic(name, tree, stateTaxa, mrcaTaxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 24 with Tree

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

the class ParsimonyStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    XMLObject cxo = xo.getChild(STATE);
    TaxonList taxa = (TaxonList) cxo.getChild(TaxonList.class);
    try {
        return new ParsimonyStatistic(name, tree, taxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 25 with Tree

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

the class RateCovarianceStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    return new RateCovarianceStatistic(name, tree, branchRateModel);
}