package dr.evomodel.treelikelihood;

import dr.evolution.LinkedGroup;
import dr.evolution.util.Taxon;
import dr.evolution.util.TaxonList;
import dr.evomodel.tree.HiddenLinkageModel;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.AbstractModelLikelihood;
import dr.inference.model.Model;
import dr.inference.model.Variable;
import dr.inference.model.Variable.ChangeType;

import java.util.ArrayList;
import java.util.Set;

/**
 * @author Aaron Darling
 */
public class HiddenLinkageLikelihood extends AbstractModelLikelihood
{

	TreeModel tree;
	HiddenLinkageModel hlm;
	

	public HiddenLinkageLikelihood(HiddenLinkageModel hlm, TreeModel tree)
	{
		super("HiddenLinkageLikelihood");
		this.hlm = hlm;
		this.tree = tree;
	}



	protected void acceptState() {
		// nothing to do
	}



	protected void handleModelChangedEvent(Model model, Object object, int index) {
		// nothing to do
	}



	protected void handleVariableChangedEvent(Variable variable, int index,
			ChangeType type) {
		// nothing to do
	}



	protected void restoreState() {
		// nothing to do
	}



	protected void storeState() {
		// nothing to do
	}



	public double getLogLikelihood() {
		double logL = 0;
		// first check whether the reads are linked together
		// according to the linkage constraints provided as data in the
		// input file
		ArrayList<LinkedGroup> linkedGroups = hlm.getData().getConstraints();
		for( LinkedGroup lg : linkedGroups ){
			TaxonList tl = lg.getLinkedReads();
			int found = 0;
			for( int l=0; l<hlm.getLinkageGroupCount(); l++ ){
				Set<Taxon> group = hlm.getGroup(l);
				for(int i=0; i<tl.getTaxonCount(); i++){
					if(group.contains(tl.getTaxon(i)))
						found++;
				}
				if(found==tl.getTaxonCount()){
					logL += Math.log(lg.getLinkageProbability());
					break;
				}else if(found>0){
					logL += Math.log(1.0-lg.getLinkageProbability());
					break;
				}
			}
		}

		// then check whether the topology of reference taxa is consistent with the fixed 
		// reference tree topology
		if(hlm.getData().getFixedReferenceTree()){
			logL += Double.NEGATIVE_INFINITY;	// not yet implemented.
		}
		return logL;
	}



	public Model getModel() {
		return this;
	}


	
	public void makeDirty() {
		// nothing to do
	}

}