import dr.inference.model.Parameter; //導入方法依賴的package包/類

@Override

public Object parseXMLObject(XMLObject xo) throws XMLParseException {

AlloppSpeciesBindings apspb = (AlloppSpeciesBindings) xo.getChild(AlloppSpeciesBindings.class);

boolean onehyb = xo.getBooleanAttribute(ONEHYBRIDIZATION);

boolean diprootisroot = xo.getBooleanAttribute(DIPLOIDROOT_ISROOT);

final XMLObject tippopxo = xo.getChild(TIP_POPULATIONS);

final double tippopvalue = tippopxo.getAttribute(Attributable.VALUE, 1.0);

final XMLObject rootpopxo = xo.getChild(ROOT_POPULATIONS);

final double rootpopvalue = rootpopxo.getAttribute(Attributable.VALUE, 1.0);

final XMLObject hybpopxo = xo.getChild(HYBRID_POPULATIONS);

final double hybpopvalue = hybpopxo.getAttribute(Attributable.VALUE, 1.0);

AlloppSpeciesNetworkModel asnm = new AlloppSpeciesNetworkModel(apspb,

tippopvalue, rootpopvalue, hybpopvalue, onehyb, diprootisroot);

// don't know dimensionality until network created, so replace parameters

ParameterParser.replaceParameter(tippopxo, asnm.tippopvalues);

final Parameter.DefaultBounds tippopbounds =

new Parameter.DefaultBounds(Double.MAX_VALUE, 0, asnm.tippopvalues.getDimension());

asnm.tippopvalues.addBounds(tippopbounds);

ParameterParser.replaceParameter(rootpopxo, asnm.rootpopvalues);

final Parameter.DefaultBounds rootpopbounds =

new Parameter.DefaultBounds(Double.MAX_VALUE, 0, asnm.rootpopvalues.getDimension());

asnm.rootpopvalues.addBounds(rootpopbounds);

ParameterParser.replaceParameter(hybpopxo, asnm.logginghybpopvalues);

final Parameter.DefaultBounds hybpopbounds =

new Parameter.DefaultBounds(Double.MAX_VALUE, 0, asnm.logginghybpopvalues.getDimension());

asnm.logginghybpopvalues.addBounds(hybpopbounds);

// note hybpopvalues are different and only work for logging.

return asnm;

}

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