package dr.inferencexml.operators; import dr.inference.model.Parameter; import dr.inference.operators.*; import dr.xml.*; /** */ public class MicrosatUpDownOperatorParser extends AbstractXMLObjectParser { public static final String MICROSAT_UP_DOWN_OPERATOR = "microsatUpDownOperator"; public static final String UP = UpDownOperatorParser.UP; public static final String DOWN = UpDownOperatorParser.DOWN; public static final String SCALE_FACTOR = ScaleOperatorParser.SCALE_FACTOR; public String getParserName() { return MICROSAT_UP_DOWN_OPERATOR; } private Scalable.Default[] getArgs(final XMLObject list) throws XMLParseException { Scalable.Default[] args = new Scalable.Default[list.getChildCount()]; for (int k = 0; k < list.getChildCount(); ++k) { final Object child = list.getChild(k); if (child instanceof Parameter) { args[k] = new Scalable.Default((Parameter) child); } } return args; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { final double scaleFactor = xo.getDoubleAttribute(SCALE_FACTOR); final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT); final CoercionMode mode = CoercionMode.parseMode(xo); final Scalable.Default[] upArgs = getArgs(xo.getChild(UP)); final Scalable.Default[] dnArgs = getArgs(xo.getChild(DOWN)); return new MicrosatUpDownOperator(upArgs, dnArgs, scaleFactor, weight, mode); } public String getParserDescription() { return "This element represents an operator that scales two parameters in different directions. " + "Each operation involves selecting a scale uniformly at random between scaleFactor and 1/scaleFactor. " + "The up parameter is multipled by this scale and the down parameter is divided by this scale."; } public Class getReturnType() { return MicrosatUpDownOperator.class; } public XMLSyntaxRule[] getSyntaxRules() { return rules; } private final XMLSyntaxRule[] ee = { new ElementRule(Parameter.class, true) }; private final XMLSyntaxRule[] rules = { AttributeRule.newDoubleRule(SCALE_FACTOR), AttributeRule.newDoubleRule(MCMCOperator.WEIGHT), AttributeRule.newBooleanRule(CoercableMCMCOperator.AUTO_OPTIMIZE, true), // Allow an arbitrary number of Parameters or Scalables in up or down new ElementRule(UP, ee, 1, Integer.MAX_VALUE), new ElementRule(DOWN, ee, 1, Integer.MAX_VALUE), }; }