use of dr.evomodel.coalescent.OldAbstractCoalescentLikelihood in project beast-mcmc by beast-dev.
the class CoalescentLikelihoodParser method parseXMLObject.
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
XMLObject cxo = xo.getChild(MODEL);
DemographicModel demoModel = (DemographicModel) cxo.getChild(DemographicModel.class);
List<TreeModel> trees = new ArrayList<TreeModel>();
List<Double> popFactors = new ArrayList<Double>();
MultiLociTreeSet treesSet = demoModel instanceof MultiLociTreeSet ? (MultiLociTreeSet) demoModel : null;
for (int k = 0; k < xo.getChildCount(); ++k) {
final Object child = xo.getChild(k);
if (child instanceof XMLObject) {
cxo = (XMLObject) child;
if (cxo.getName().equals(POPULATION_TREE)) {
final TreeModel t = (TreeModel) cxo.getChild(TreeModel.class);
assert t != null;
trees.add(t);
popFactors.add(cxo.getAttribute(POPULATION_FACTOR, 1.0));
}
}
// in the future we may have arbitrary multi-loci element
// else if( child instanceof MultiLociTreeSet ) {
// treesSet = (MultiLociTreeSet)child;
// }
}
TreeModel treeModel = null;
if (trees.size() == 1 && popFactors.get(0) == 1.0) {
treeModel = trees.get(0);
} else if (trees.size() > 1) {
treesSet = new MultiLociTreeSet.Default(trees, popFactors);
} else if (!(trees.size() == 0 && treesSet != null)) {
throw new XMLParseException("Incorrectly constructed likelihood element");
}
TaxonList includeSubtree = null;
if (xo.hasChildNamed(INCLUDE)) {
includeSubtree = (TaxonList) xo.getElementFirstChild(INCLUDE);
}
List<TaxonList> excludeSubtrees = new ArrayList<TaxonList>();
if (xo.hasChildNamed(EXCLUDE)) {
cxo = xo.getChild(EXCLUDE);
for (int i = 0; i < cxo.getChildCount(); i++) {
excludeSubtrees.add((TaxonList) cxo.getChild(i));
}
}
if (treeModel != null) {
try {
return new CoalescentLikelihood(treeModel, includeSubtree, excludeSubtrees, demoModel);
} catch (TreeUtils.MissingTaxonException mte) {
throw new XMLParseException("treeModel missing a taxon from taxon list in " + getParserName() + " element");
}
} else {
if (includeSubtree != null || excludeSubtrees.size() > 0) {
throw new XMLParseException("Include/Exclude taxa not supported for multi locus sets");
}
// a base - and modifing it will probsbly result in a bigger mess.
return new OldAbstractCoalescentLikelihood(treesSet, demoModel);
}
}
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