public class BinomialLikelihoodParser extends AbstractXMLObjectParser {
public static final String TRIALS = "trials";
public static final String COUNTS = "counts";
public static final String PROPORTION = "proportion";
public static final String VALUES = "values";
public static final String ON_LOGIT_SCALE = "onLogitScale";
public String getParserName() {
return BinomialLikelihood.BINOMIAL_LIKELIHOOD;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final boolean onLogitScale = xo.getAttribute(ON_LOGIT_SCALE, false);
XMLObject cxo = xo.getChild(COUNTS);
Parameter countsParam = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(PROPORTION);
Parameter proportionParam = (Parameter) cxo.getChild(Parameter.class);
if (proportionParam.getDimension() != 1
&& proportionParam.getDimension() != countsParam.getDimension()) {
throw new XMLParseException(
"Proportion dimension ("
+ proportionParam.getDimension()
+ ") "
+ "must equal 1 or counts dimension ("
+ countsParam.getDimension()
+ ")");
}
cxo = xo.getChild(TRIALS);
Parameter trialsParam;
if (cxo.hasAttribute(VALUES)) {
int[] tmp = cxo.getIntegerArrayAttribute(VALUES);
double[] v = new double[tmp.length];
for (int i = 0; i < tmp.length; ++i) {
v[i] = tmp[i];
}
trialsParam = new Parameter.Default(v);
} else {
trialsParam = (Parameter) cxo.getChild(Parameter.class);
}
if (trialsParam.getDimension() != countsParam.getDimension()) {
throw new XMLParseException(
"Trials dimension ("
+ trialsParam.getDimension()
+ ") must equal counts dimension ("
+ countsParam.getDimension()
+ ")");
}
return new BinomialLikelihood(trialsParam, proportionParam, countsParam, onLogitScale);
}
// ************************************************************************
// AbstractXMLObjectParser implementation
// ************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newBooleanRule(ON_LOGIT_SCALE, true),
new ElementRule(COUNTS, new XMLSyntaxRule[] {new ElementRule(Parameter.class)}),
new ElementRule(PROPORTION, new XMLSyntaxRule[] {new ElementRule(Parameter.class)}),
new XORRule(
new ElementRule(
TRIALS,
new XMLSyntaxRule[] {
AttributeRule.newIntegerArrayRule(VALUES, false),
}),
new ElementRule(TRIALS, new XMLSyntaxRule[] {new ElementRule(Parameter.class)})),
};
public String getParserDescription() {
return "Calculates the likelihood of some data given some parametric or empirical distribution.";
}
public Class getReturnType() {
return Likelihood.class;
}
}
