package dr.evomodel.antigenic.phyloClustering.statistics;

import java.util.LinkedList;

import dr.evolution.tree.NodeRef;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.*;
import dr.xml.*;

/**
 *  @author Charles Cheung
 * @author Trevor Bedford
 */

public class muStatistic extends Statistic.Abstract implements VariableListener {

	static  int MAX_DIM = 30;
	

	private MatrixParameter mu;
    private TreeModel treeModel;
    private Parameter indicators;
    
    public static final String MU_STATISTIC = "muStatistic";

    public muStatistic( TreeModel tree, MatrixParameter mu, Parameter indicators) {
        
        this.treeModel = tree;
        this.mu = mu;
        this.indicators = indicators;
        
        mu.addParameterListener(this);
        indicators.addParameterListener(this);
    }
    


    public int getDimension() {
        return treeModel.getNodeCount()*2;
    }



    //assume print in order... so before printing the first number, 
    //determine all the nodes that are active.
    public double getStatisticValue(int dim) {

    	int curNode = dim/2;
    	double value = mu.getParameter(curNode).getParameterValue(dim % 2);
    	
    	//if((int) indicators.getParameterValue(curNode)  == 0){
    	//	value = 0;
    	//}
          return (  value );

    }

    
    
     
    
    
    public String getDimensionName(int dim) {
    	String name = "mu_" +  ((dim/2) )  + "-" + ((dim %2 ) +1 );
        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 MU_STRING = "mu";
        public final static String INDICATORS_STRING = "indicators";

        public String getParserName() {
            return MU_STATISTIC;
        }

        public Object parseXMLObject(XMLObject xo) throws XMLParseException {
            TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
            MatrixParameter muParam = (MatrixParameter) xo.getElementFirstChild(MU_STRING);
            Parameter indicators = (Parameter) xo.getElementFirstChild(INDICATORS_STRING);

            return new muStatistic( treeModel, muParam, 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 muStatistic.class;
        }

        public XMLSyntaxRule[] getSyntaxRules() {
            return rules;
        }

        private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
            new ElementRule(TreeModel.class),
            new ElementRule(MU_STRING, Parameter.class),
            new ElementRule(INDICATORS_STRING, Parameter.class)

        };
    };

    

}