package dr.evomodelxml.operators; import dr.evomodel.operators.MulTreeNodeSlide; import dr.evomodel.speciation.MulSpeciesBindings; import dr.evomodel.speciation.MulSpeciesTreeModel; import dr.inference.operators.MCMCOperator; import dr.xml.*; /** * * @author Graham Jones * Date: 20/12/2011 */ public class MulTreeNodeSlideParser extends AbstractXMLObjectParser { public static final String MULTREE_NODE_REHEIGHT = "mulTreeNodeReHeight"; public String getParserName() { return MULTREE_NODE_REHEIGHT; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { MulSpeciesBindings species = (MulSpeciesBindings) xo.getChild(MulSpeciesBindings.class); MulSpeciesTreeModel tree = (MulSpeciesTreeModel) xo.getChild(MulSpeciesTreeModel.class); final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); // final double range = xo.getAttribute("range", 1.0); // if( range <= 0 || range > 1.0 ) { // throw new XMLParseException("range out of range"); // } //final boolean oo = xo.getAttribute("outgroup", false); return new MulTreeNodeSlide(tree, species /*, range*//*, oo*/, weight); } public String getParserDescription() { return "Specialized Species tree operator, transform tree without breaking embedding of gene trees."; } public Class getReturnType() { return MulTreeNodeSlide.class; } public XMLSyntaxRule[] getSyntaxRules() { return new XMLSyntaxRule[]{ AttributeRule.newDoubleRule(MCMCOperator.WEIGHT), // AttributeRule.newDoubleRule("range", true), // AttributeRule.newBooleanRule("outgroup", true), new ElementRule(MulSpeciesBindings.class), new ElementRule(MulSpeciesTreeModel.class) }; } }