public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[] {
AttributeRule.newBooleanRule(BeagleTreeLikelihoodParser.USE_AMBIGUITIES, true),
AttributeRule.newStringRule(RECONSTRUCTION_TAG_NAME, true),
AttributeRule.newBooleanRule(INTEGRATE_GAIN_RATE),
new ElementRule(
IMMIGRATION_RATE, new XMLSyntaxRule[] {new ElementRule(Parameter.class)}, true),
new ElementRule(PatternList.class),
new ElementRule(TreeModel.class),
new ElementRule(GammaSiteRateModel.class),
new ElementRule(BranchModel.class, true),
new ElementRule(BranchRateModel.class, true),
new ElementRule(TipStatesModel.class, true),
new ElementRule(SubstitutionModel.class, true),
AttributeRule.newStringRule(BeagleTreeLikelihoodParser.SCALING_SCHEME, true),
new ElementRule(
PARTIALS_RESTRICTION,
new XMLSyntaxRule[] {
new ElementRule(TaxonList.class), new ElementRule(Parameter.class),
},
true),
new ElementRule(
OBSERVATION_PROCESS,
new XMLSyntaxRule[] {
AttributeRule.newStringRule(OBSERVATION_TYPE, false),
AttributeRule.newStringRule(OBSERVATION_TAXON, true)
})
};
}
public class TreeLengthStatisticParser extends AbstractXMLObjectParser {
public static final String TREE_LENGTH_STATISTIC = "treeLengthStatistic";
public String getParserName() {
return TREE_LENGTH_STATISTIC;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
String name = xo.getAttribute(Statistic.NAME, xo.getId());
Tree tree = (Tree) xo.getChild(Tree.class);
return new TreeLengthStatistic(name, tree);
}
// ************************************************************************
// AbstractXMLObjectParser implementation
// ************************************************************************
public String getParserDescription() {
return "A statistic that returns the average of the branch rates";
}
public Class getReturnType() {
return TreeLengthStatistic.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newStringRule(Statistic.NAME, true), new ElementRule(TreeModel.class),
};
}
