package dr.evomodel.antigenic.phyloClustering.MCMCOperators;
import dr.evomodel.antigenic.phyloClustering.Tree_Clustering_Shared_Routines;
import dr.evomodel.tree.TreeModel;
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 serumDriftActiveScaledMu1Operator extends AbstractCoercableOperator {
private MatrixParameter mu = null;
private Parameter serumDrift = null;
private MatrixParameter virusLocations = null;
private MatrixParameter virusLocationsTreeNode = null;
private Parameter indicators;
private TreeModel treeModel;
private int numdata;
private int numNodes;
private int []correspondingTreeIndexForVirus = null; //relates treeModels's indexing system to cluster label's indexing system of viruses. Gets assigned
private double scaleFactor;
public serumDriftActiveScaledMu1Operator(double weight, MatrixParameter virusLocations, MatrixParameter mu, Parameter indicators, Parameter serumDrift, TreeModel treeModel_in, double scale, MatrixParameter virusLocationsTreeNode_in){
super(CoercionMode.COERCION_ON);
setWeight(weight);
this.virusLocations = virusLocations;
this.mu = mu;
this.indicators = indicators;
this.serumDrift = serumDrift;
this.treeModel= treeModel_in;
this.scaleFactor = scale;
this.virusLocationsTreeNode = virusLocationsTreeNode_in;
numNodes = treeModel.getNodeCount();
numdata = virusLocations.getColumnDimension();
correspondingTreeIndexForVirus = Tree_Clustering_Shared_Routines.setMembershipTreeToVirusIndexes(numdata, virusLocations, numNodes, treeModel);
Tree_Clustering_Shared_Routines.updateUndriftedVirusLocations(numNodes, numdata, treeModel, virusLocationsTreeNode, indicators, mu, virusLocations, correspondingTreeIndexForVirus);
}
public double doOperation() {
final double scale = (scaleFactor + (MathUtils.nextDouble() * ((1.0 / scaleFactor) - scaleFactor)));
//change serum drift
//double WALK_SIZE = 0.2; //when the walk size becomes 0.5, .... things become weird.. too big
//double change = Math.random()*WALK_SIZE- WALK_SIZE/2 ;
double original_serumDrift_Val = serumDrift.getParameterValue(0);
// System.out.println("original_serumDrift_Val = " + original_serumDrift_Val);
//double new_serumDrift_Val = change + original_serumDrift_Val;
double new_serumDrift_Val = scale * original_serumDrift_Val;
serumDrift.setParameterValue(0, new_serumDrift_Val);
// System.out.println("new_serumDrift_Val=" + serumDrift.getParameterValue(0));
//make sure all the active mu's first dimension stays intact
for(int i=0; i < numNodes; i++){
if( (int) indicators.getParameterValue(i) == 1){
double oldValue = mu.getParameter(i).getParameterValue(0);
double newValue = oldValue * new_serumDrift_Val/original_serumDrift_Val;
mu.getParameter(i).setParameterValue(0, newValue);
// System.out.println("indicator" + i + " oldValue = " + oldValue + " and newValue=" + mu.getParameter(i).getParameterValue(0));
}
}
//the virus location needs to be updated because the mu's are updated
Tree_Clustering_Shared_Routines.updateUndriftedVirusLocations(numNodes, numdata, treeModel, virusLocationsTreeNode, indicators, mu, virusLocations, correspondingTreeIndexForVirus);
double logq = -Math.log(scale);
// System.out.println("logq=" + logq);
// System.out.println("================================================");
//return 0;
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 String getPerformanceSuggestion() {
if (Utils.getAcceptanceProbability(this) < getMinimumAcceptanceLevel()) {
return "";
} else if (Utils.getAcceptanceProbability(this) > getMaximumAcceptanceLevel()) {
return "";
} else {
return "";
}
}
public final void optimize(double targetProb) {
throw new RuntimeException("This operator cannot be optimized!");
}
public boolean isOptimizing() {
return false;
}
public void setOptimizing(boolean opt) {
throw new RuntimeException("This operator cannot be optimized!");
}
public double getMinimumAcceptanceLevel() {
return 0.1;
}
public double getMaximumAcceptanceLevel() {
return 0.4;
}
public double getMinimumGoodAcceptanceLevel() {
return 0.20;
}
public double getMaximumGoodAcceptanceLevel() {
return 0.30;
}
*/
public final static String SERUMDRIFTACTIVESCALEDMU1Operator = "serumDriftActiveScaledMu1Operator";
public final String getOperatorName() {
return SERUMDRIFTACTIVESCALEDMU1Operator;
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public final static String VIRUSLOCATIONS = "virusLocations";
public final static String VIRUSLOCATIONSTREENODE = "virusLocationsTreeNodes";
public final static String MU = "mu";
public final static String SERUMDRIFT = "serumDrift";
public final static String INDICATORS = "indicators";
public final static String SCALE = "scaleFactor";
public String getParserName() {
return SERUMDRIFTACTIVESCALEDMU1Operator;
}
/* (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(VIRUSLOCATIONS);
MatrixParameter virusLocations = (MatrixParameter) cxo.getChild(MatrixParameter.class);
cxo = xo.getChild(VIRUSLOCATIONSTREENODE);
MatrixParameter virusLocationsTreeNode = (MatrixParameter) cxo.getChild(MatrixParameter.class);
cxo = xo.getChild(MU);
MatrixParameter mu = (MatrixParameter) cxo.getChild(MatrixParameter.class);
cxo = xo.getChild(INDICATORS);
Parameter indicators = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(SERUMDRIFT);
Parameter serumDrift = (Parameter) cxo.getChild(Parameter.class);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
return new serumDriftActiveScaledMu1Operator(weight, virusLocations, mu, indicators, serumDrift, treeModel, scale, virusLocationsTreeNode);
}
//************************************************************************
// 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(VIRUSLOCATIONS, Parameter.class),
new ElementRule(VIRUSLOCATIONSTREENODE, MatrixParameter.class),
new ElementRule(MU, Parameter.class),
new ElementRule(INDICATORS, Parameter.class),
new ElementRule(SERUMDRIFT, Parameter.class),
new ElementRule(TreeModel.class),
};
};
public int getStepCount() {
return 1;
}
}