Examples with XMLParseException dr.xml.XMLParseException used on opensource projects

Example 6 with XMLParseException

use of dr.xml.XMLParseException in project beast-mcmc by beast-dev.

the class IndependentCoalescentSampler method doOperation.

/**
 * change the parameter and return the hastings ratio.
 */
public double doOperation() {
    CoalescentSimulator simulator = new CoalescentSimulator();
    List<TaxonList> taxonLists = new ArrayList<TaxonList>();
    double rootHeight = -1.0;
    double oldLikelihood = 0.0;
    double newLikelihood = 0.0;
    // should have one child that is node
    for (int i = 0; i < xo.getChildCount(); i++) {
        final Object child = xo.getChild(i);
        // careful: Trees are TaxonLists ... (AER); see OldCoalescentSimulatorParser
        if (child instanceof Tree) {
        // do nothing
        } else if (child instanceof TaxonList) {
            // taxonLists.add((TaxonList) child);
            taxonLists.add((Taxa) child);
            // taxa added
            break;
        }
    }
    try {
        Tree[] trees = new Tree[taxonLists.size()];
        // simulate each taxonList separately
        for (int i = 0; i < taxonLists.size(); i++) {
            trees[i] = simulator.simulateTree(taxonLists.get(i), demoModel);
        }
        oldLikelihood = coalescent.getLogLikelihood();
        SimpleTree simTree = simulator.simulateTree(trees, demoModel, rootHeight, trees.length != 1);
        // this would be the normal way to do it
        treeModel.beginTreeEdit();
        // now it's allowed to adjust the tree structure
        treeModel.adoptTreeStructure(simTree);
        // endTreeEdit() would then fire the events
        treeModel.endTreeEdit();
        newLikelihood = coalescent.getLogLikelihood();
    } catch (IllegalArgumentException iae) {
        try {
            throw new XMLParseException(iae.getMessage());
        } catch (XMLParseException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    return oldLikelihood - newLikelihood;
}

Example 7 with XMLParseException

use of dr.xml.XMLParseException in project beast-mcmc by beast-dev.

the class EpochBranchModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Logger.getLogger("dr.evomodel").info("\nUsing multi-epoch branch model.");
    MutableTreeModel treeModel = (MutableTreeModel) xo.getChild(MutableTreeModel.class);
    SubstitutionModel ancestralSubstitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
    List<Epoch> epochs = new ArrayList<Epoch>();
    for (int i = 0; i < xo.getChildCount(); i++) {
        if (xo.getChild(i) instanceof XMLObject) {
            XMLObject xoc = (XMLObject) xo.getChild(i);
            if (xoc.getName().equals(EPOCH)) {
                Parameter tt = null;
                if (xoc.hasAttribute(TRANSITION_TIME)) {
                    double t = xoc.getAttribute(TRANSITION_TIME, 0.0);
                    tt = new Parameter.Default(1, t);
                }
                SubstitutionModel s = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
                if (xoc.hasChildNamed(TRANSITION_TIME)) {
                    if (tt != null) {
                        throw new XMLParseException("An epoch cannot have a transitionTime attribute and a parameter");
                    }
                    tt = (Parameter) xoc.getElementFirstChild(TRANSITION_TIME);
                }
                epochs.add(new Epoch(s, tt));
            }
        }
    }
    Collections.sort(epochs);
    List<SubstitutionModel> substitutionModels = new ArrayList<SubstitutionModel>();
    CompoundParameter transitionTimes = new CompoundParameter("epochTimes");
    for (Epoch epoch : epochs) {
        substitutionModels.add(epoch.substitutionModel);
        transitionTimes.addParameter(epoch.timeParameter);
    }
    substitutionModels.add(ancestralSubstitutionModel);
    return new EpochBranchModel(treeModel, substitutionModels, transitionTimes);
}