@Override
public double doOperation() throws OperatorFailedException {
apspnet.beginNetworkEdit();
apspnet.moveLegs();
apspnet.endNetworkEdit();
return 0;
}
@Override
public double doOperation() throws OperatorFailedException {
apspnet.beginNetworkEdit();
double b = (1.0 - scalingFactor) * (1.0 - scalingFactor) / scalingFactor;
double c = scalingFactor / (1.0 - scalingFactor);
double y = MathUtils.nextDouble();
double s = b * (y + c) * (y + c);
int i = MathUtils.nextInt(apspnet.getNumberOfTetraTrees());
apspnet.setOneHybPopValue(i, s * apspnet.getOneHybPopValue(i));
apspnet.endNetworkEdit();
return 0.0; // this way of scaling, with proposal proportional to x^-(1/2) has hastings ratio 1
}
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
AlloppSpeciesBindings apsp = (AlloppSpeciesBindings) xo.getChild(AlloppSpeciesBindings.class);
AlloppSpeciesNetworkModel apspnet =
(AlloppSpeciesNetworkModel) xo.getChild(AlloppSpeciesNetworkModel.class);
if (apspnet.getOneHybridization()) {
throw new XMLParseException(
"oneHybridization is set to true but there is a changeNumHybridizations operator");
}
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
return new AlloppChangeNumHybridizations(apspnet, apsp, weight);
}
@Override
public String getOperatorName() {
return AlloppHybPopSizesScaleParser.HYB_POP_SIZES_SCALE
+ "("
+ apspnet.getId()
+ ","
+ apsp.getId()
+ ")";
}
@Override
public String getOperatorName() {
return AlloppMoveLegsParser.MOVE_LEGS + "(" + apspnet.getId() + "," + apsp.getId() + ")";
}