package dr.evomodel.antigenic.phyloClustering.misc.obsolete;
import dr.evomodel.antigenic.phyloClustering.MCMCOperators.serumDriftActiveScaledMu1Operator;
import dr.inference.model.MatrixParameter;
import dr.inference.model.Parameter;
import dr.inference.operators.AbstractCoercableOperator;
import dr.inference.operators.CoercionMode;
import dr.inference.operators.MCMCOperator;
import dr.inference.operators.OperatorUtils;
import dr.math.MathUtils;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.AttributeRule;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLObjectParser;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
public class serumDriftScalingMuOperator extends AbstractCoercableOperator {
private Parameter serumDrift = null;
private MatrixParameter mu = null;
private Parameter muMean = null;
private Parameter muPrec = null;
private double scaleFactor;
public serumDriftScalingMuOperator(double weight, MatrixParameter mu, Parameter muMean, Parameter muPrec, Parameter serumDrift, double scale){
super(CoercionMode.COERCION_ON);
setWeight(weight);
this.mu = mu;
this.muMean = muMean;
this.muPrec = muPrec;
this.serumDrift = serumDrift;
this.scaleFactor = scale;
}
public double doOperation() {
final double scale = (scaleFactor + (MathUtils.nextDouble() * ((1.0 / scaleFactor) - scaleFactor)));
// System.out.println("serumDriftScaling operator ran");
// System.out.println("scale=" + scale);
//changing serum drift
serumDrift.setParameterValue(0, scale *serumDrift.getParameterValue(0) );
//changing mu
//System.out.println("dimension=" + mu.getColumnDimension());
for(int i=0; i < mu.getColumnDimension(); i++){
Parameter m = mu.getParameter(i);
m.setParameterValue(0, scale*m.getParameterValue(0));
}
//changing muMean
muMean.setParameterValue(0, scale*muMean.getParameterValue(0));
//changing muPrec
muPrec.setParameterValue(0, scale*scale*muPrec.getParameterValue(0));
double logq = -Math.log(scale);
return logq;
}
//copied from the original ScaleOperator
public double getCoercableParameter() {
return Math.log(1.0 / scaleFactor - 1.0);
}
//copied from the original ScaleOperator
public void setCoercableParameter(double value) {
scaleFactor = 1.0 / (Math.exp(value) + 1.0);
}
//copied from the original ScaleOperator
public double getRawParameter() {
return scaleFactor;
}
//copied from the original ScaleOperator
public double getTargetAcceptanceProbability() {
return 0.234;
}
//copied from the original ScaleOperator
public final String getPerformanceSuggestion() {
double prob = MCMCOperator.Utils.getAcceptanceProbability(this);
double targetProb = getTargetAcceptanceProbability();
dr.util.NumberFormatter formatter = new dr.util.NumberFormatter(5);
double sf = OperatorUtils.optimizeScaleFactor(scaleFactor, prob, targetProb);
if (prob < getMinimumGoodAcceptanceLevel()) {
return "Try setting scaleFactor to about " + formatter.format(sf);
} else if (prob > getMaximumGoodAcceptanceLevel()) {
return "Try setting scaleFactor to about " + formatter.format(sf);
} else return "";
}
public final static String SERUMDRIFTSCALINGMUOperator = "serumDriftScalingMuOperator";
public final String getOperatorName() {
return SERUMDRIFTSCALINGMUOperator;
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public final static String SCALE = "scaleFactor";
public final static String MU = "mu";
public final static String SERUMDRIFT = "serumDrift";
public final static String MUMEAN = "muMean";
public final static String MUPREC = "muPrec";
public String getParserName() {
return SERUMDRIFTSCALINGMUOperator;
}
/* (non-Javadoc)
* @see dr.xml.AbstractXMLObjectParser#parseXMLObject(dr.xml.XMLObject)
*/
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
double scale = xo.getDoubleAttribute(SCALE);
XMLObject cxo = xo.getChild(MU);
MatrixParameter mu = (MatrixParameter) cxo.getChild(MatrixParameter.class);
cxo = xo.getChild(SERUMDRIFT);
Parameter serumDrift = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(MUMEAN);
Parameter muMean = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(MUPREC);
Parameter muPrec = (Parameter) cxo.getChild(Parameter.class);
return new serumDriftScalingMuOperator(weight, mu, muMean, muPrec, serumDrift, scale);
// public serumDriftScalingMuOperator(double weight, MatrixParameter mu, Parameter muMean, Parameter muPrec, Parameter serumDrift, double scale){
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "changes serum drift and make sure the first dimension of the active drifted mus stay the same";
}
public Class getReturnType() {
return serumDriftActiveScaledMu1Operator.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
AttributeRule.newDoubleRule(SCALE),
new ElementRule(MU, Parameter.class),
new ElementRule(MUMEAN, Parameter.class),
new ElementRule(MUPREC, Parameter.class),
new ElementRule(SERUMDRIFT, Parameter.class),
};
};
public int getStepCount() {
return 1;
}
}