@Override
protected boolean requiresRecalculation() {
final TreeIntervals ti = treeIntervalsInput.get();
if (ti != null) {
// boolean d = ti.isDirtyCalculation();
// assert d;
assert ti.isDirtyCalculation();
return true;
}
return treeInput.get().somethingIsDirty();
}
@Override
public void initAndValidate() throws Exception {
popFunction = popFunctionInput.get();
popSizesBottom = popSizesBottomInput.get();
popSizesTop = popSizesTopInput.get();
// set up sizes of population functions
final int nSpecies = treeInput.get().getLeafNodeCount();
final int nNodes = treeInput.get().getNodeCount();
switch (popFunction) {
case constant:
popSizesBottom.setDimension(nNodes);
break;
case linear:
if (popSizesTop == null) {
throw new Exception("topPopSize must be specified");
}
popSizesBottom.setDimension(nSpecies);
popSizesTop.setDimension(nNodes);
break;
case linear_with_constant_root:
if (popSizesTop == null) {
throw new Exception("topPopSize must be specified");
}
popSizesBottom.setDimension(nSpecies);
popSizesTop.setDimension(nNodes - 1);
break;
}
// bottom prior = Gamma(2,Psi)
gamma2Prior = new Gamma();
gamma2Prior.betaInput.setValue(gammaParameterInput.get(), gamma2Prior);
// top prior = Gamma(4,Psi)
gamma4Prior = new Gamma();
final RealParameter parameter = new RealParameter(new Double[] {4.0});
gamma4Prior.alphaInput.setValue(parameter, gamma4Prior);
gamma4Prior.betaInput.setValue(gammaParameterInput.get(), gamma4Prior);
if (popFunction != PopSizeFunction.constant && gamma4Prior == null) {
throw new Exception("Top prior must be specified when population function is not constant");
}
// make sure the m_taxonSet is a set of taxonsets
// HACK to make Beauti initialise: skip the check here
// for (Taxon taxon : m_taxonSet.get().m_taxonset.get()) {
// if (!(taxon instanceof TaxonSet)) {
// throw new Exception("taxonset should be sets of taxa only, not individual taxons");
// }
// }
}
@Override
public void initAndValidate() throws Exception {
_lower = lowerInput.get();
_upper = upperInput.get();
if (_lower >= _upper) {
throw new Exception("Upper value should be higher than lower value");
}
distr.setBounds(_lower, _upper);
infiniteSupport = Double.isInfinite(_lower) || Double.isInfinite(_upper);
if (infiniteSupport) {
density = 1.0;
} else {
density = 1.0 / (_upper - _lower);
}
}