package dr.evomodel.antigenic.phyloClustering.statistics;
import dr.inference.model.*;
import dr.xml.*;
/**
* @author Charles Cheung
* @author Trevor Bedford
*/
public class KStatistic extends Statistic.Abstract implements VariableListener {
public static final String K_STATISTIC = "KStatistic";
public KStatistic(Parameter indicators) {
this.indicatorsParameter = indicators;
indicatorsParameter.addParameterListener(this);
}
public int getDimension() {
return 1;
}
//assume print in order... so before printing the first number,
//determine all the nodes that are active.
public double getStatisticValue(int dim) {
double count = 0;
for(int i=0; i < indicatorsParameter.getDimension(); i++){
if( (int) indicatorsParameter.getParameterValue(i) == 1 ){
count++;
}
}
return count;
}
public String getDimensionName(int dim) {
String name = "K";
return name;
}
public void variableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
// do nothing
//System.out.println("hi got printed");
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public final static String INDICATORS = "indicators";
public String getParserName() {
return K_STATISTIC;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Parameter indicators = (Parameter) xo.getElementFirstChild(INDICATORS);
return new KStatistic(indicators);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element returns a statistic that shifts a matrix of locations by location drift in the first dimension.";
}
public Class getReturnType() {
return KStatistic.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(INDICATORS, Parameter.class)
};
};
private Parameter indicatorsParameter;
}