Examples with UncertainSiteList dr.evolution.alignment.UncertainSiteList used on opensource projects

Example 1 with UncertainSiteList

use of dr.evolution.alignment.UncertainSiteList in project beast-mcmc by beast-dev.

the class UncertainAttributePatternsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String attributeName = xo.getStringAttribute(ATTRIBUTE);
    TaxonList taxa = (TaxonList) xo.getChild(TaxonList.class);
    DataType dataType = DataTypeUtils.getDataType(xo);
    if (dataType == null) {
        throw new XMLParseException("dataType expected for attributePatterns element");
    }
    // using a SimpleSiteList rather than Patterns to allow ancestral reconstruction
    UncertainSiteList patterns = new UncertainSiteList(dataType, taxa);
    boolean normalize = xo.getAttribute(NORMALIZE, true);
    if (dataType == null) {
        // TODO Is this necessary given XMLSyntaxRules?
        throw new XMLParseException("dataType expected for attributePatterns element");
    }
    double[][] uncertainPattern = new double[taxa.getTaxonCount()][];
    // Parse attributes
    boolean attributeFound = false;
    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Taxon taxon = taxa.getTaxon(i);
        Object value = taxon.getAttribute(attributeName);
        if (value != null) {
            attributeFound = true;
            List<StateProbability> stateProbabilities;
            try {
                stateProbabilities = parseStates(value.toString(), dataType);
            } catch (StateParseException e) {
                throw new XMLParseException("State or probability for attribute (" + attributeName + ") in taxon " + taxon.getId() + " is invalid; state = \"" + e.getState() + "\" and probability =\"" + e.getProbability() + "\"");
            }
            uncertainPattern[i] = convertToPartials(stateProbabilities, dataType, normalize);
        } else {
            throw new XMLParseException("State for attribute (" + attributeName + ") in taxon " + taxon.getId() + " is unknown.");
        }
    }
    if (!attributeFound) {
        throw new XMLParseException("The attribute (" + attributeName + ") was missing in all taxa. Check the name of the attribute.");
    }
    patterns.addPattern(uncertainPattern);
    Logger.getLogger("dr.evolution").info("\n ---------------------------------\nCreating an uncertain attribute model for attribute \"" + attributeName + "\"");
    Logger.getLogger("dr.evolution").info("\tIf you publish results using this model, please reference:");
    Logger.getLogger("dr.evolution").info("\t" + Citable.Utils.getCitationString(patterns));
    Logger.getLogger("dr.evolution").info("\n");
    return patterns;
}