package dr.evomodel.antigenic.phyloClustering.MCMCOperators;
import java.util.LinkedList;
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 RandomWalkOnActiveMu extends AbstractCoercableOperator {
private MatrixParameter mu = 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 windowSize = 0.5;
public RandomWalkOnActiveMu(double weight, MatrixParameter virusLocations, MatrixParameter mu, Parameter indicators, TreeModel treeModel_in, double windowSize, MatrixParameter virusLocationsTreeNode_in){
super(CoercionMode.COERCION_ON);
setWeight(weight);
this.windowSize = windowSize;
this.virusLocations = virusLocations;
this.mu = mu;
this.indicators = indicators;
this.treeModel= treeModel_in;
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() {
//first, randomly select an "on" node to overwrite
int originalNode = Tree_Clustering_Shared_Routines.findAnOnNodeIncludingRootRandomly(numNodes, indicators); //find an on-node
//unbounded walk
int dimSelect = (int) Math.floor( Math.random()* 2 );
double change = (2.0 * MathUtils.nextDouble() - 1.0) * windowSize;
double originalValue = mu.getParameter(originalNode).getParameterValue(dimSelect);
mu.getParameter(originalNode ).setParameterValue(dimSelect, originalValue + change);
//a. by removing the selected node, each child of this node should be updated to keep the absolute location of
//the child cluster fixed as before
LinkedList<Integer> childrenOriginalNode = Tree_Clustering_Shared_Routines.findActiveBreakpointsChildren(originalNode, numNodes, treeModel, indicators);
for(int i=0; i < childrenOriginalNode.size(); i++){
int muIndexNum = childrenOriginalNode.get(i).intValue() ;
Parameter curMu = mu.getParameter( muIndexNum );
double curMu_original = curMu.getParameterValue( dimSelect);
mu.getParameter(muIndexNum).setParameterValue(dimSelect, curMu_original - change);
}
//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);
return 0.0;
}
//MCMCOperator INTERFACE
public double getCoercableParameter() {
return Math.log(windowSize);
}
public void setCoercableParameter(double value) {
windowSize = Math.exp(value);
}
public double getRawParameter() {
return windowSize;
}
public double getTargetAcceptanceProbability() {
return 0.234;
}
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 String getPerformanceSuggestion() {
double prob = MCMCOperator.Utils.getAcceptanceProbability(this);
double targetProb = getTargetAcceptanceProbability();
double ws = OperatorUtils.optimizeWindowSize(windowSize, prob, targetProb);
if (prob < getMinimumGoodAcceptanceLevel()) {
return "Try decreasing windowSize to about " + ws;
} else if (prob > getMaximumGoodAcceptanceLevel()) {
return "Try increasing windowSize to about " + ws;
} else return "";
}
public final static String RANDOMWALKACTIVEMU = "randomWalkOnActiveMu";
public final String getOperatorName() {
return RANDOMWALKACTIVEMU;
}
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 INDICATORS = "indicators";
public final static String WINDOWSIZE = "windowSize";
public String getParserName() {
return RANDOMWALKACTIVEMU;
}
/* (non-Javadoc)
* @see dr.xml.AbstractXMLObjectParser#parseXMLObject(dr.xml.XMLObject)
*/
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
double windowSize = xo.getDoubleAttribute(WINDOWSIZE);
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);
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
return new RandomWalkOnActiveMu(weight, virusLocations, mu, indicators, treeModel, windowSize, 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 RandomWalkOnActiveMu.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
AttributeRule.newDoubleRule(WINDOWSIZE),
new ElementRule(VIRUSLOCATIONS, Parameter.class),
new ElementRule(VIRUSLOCATIONSTREENODE, MatrixParameter.class),
new ElementRule(MU, Parameter.class),
new ElementRule(INDICATORS, Parameter.class),
new ElementRule(TreeModel.class),
};
};
public int getStepCount() {
return 1;
}
}