package dr.evomodelxml.operators;
import dr.evomodel.operators.AlloppNetworkNodeSlide;
import dr.evomodel.operators.TreeNodeSlide;
import dr.evomodel.speciation.AlloppSpeciesBindings;
import dr.evomodel.speciation.AlloppSpeciesNetworkModel;
import dr.evomodel.speciation.SpeciesBindings;
import dr.evomodel.speciation.SpeciesTreeModel;
import dr.inference.operators.MCMCOperator;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.AttributeRule;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
/**
*
* @author Graham Jones
* Date: 01/07/2011
*/
/*
<networkNodeReHeight weight="94">
<alloppSpecies idref="alloppSpecies"/>
<alloppSpeciesNetwork idref="apspnetwork"/>
</networkNodeReHeight>
*/
public class AlloppNetworkNodeSlideParser extends AbstractXMLObjectParser {
public static final String NETWORK_NODE_REHEIGHT = "networkNodeReHeight";
public String getParserName() {
return NETWORK_NODE_REHEIGHT;
}
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
AlloppSpeciesBindings apsp = (AlloppSpeciesBindings) xo.getChild(AlloppSpeciesBindings.class);
AlloppSpeciesNetworkModel apspnet = (AlloppSpeciesNetworkModel) xo.getChild(AlloppSpeciesNetworkModel.class);
final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
return new AlloppNetworkNodeSlide(apspnet, apsp, weight);
}
@Override
public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
new ElementRule(AlloppSpeciesBindings.class),
new ElementRule(AlloppSpeciesNetworkModel.class)
};
}
@Override
public String getParserDescription() {
return "Operator for allopolyploid species network: transforms network without breaking embedding of gene trees.";
}
@Override
public Class getReturnType() {
return AlloppNetworkNodeSlide.class;
}
}