DicebyClusterID.java

package operonClustering;

import genomeObjects.GenomicElement;
import genomeObjects.GenomicElementAndQueryMatch;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;

public class DicebyClusterID implements OperonDissimilarityMeasure{

		@Override
		public double computeDissimilarity(LinkedList<GenomicElementAndQueryMatch> O1, LinkedList<GenomicElementAndQueryMatch> O2) {
			
			//initialize lists
			ArrayList<Integer> O1Values = new ArrayList<Integer>();
			ArrayList<Integer> O2Values = new ArrayList<Integer>();
			
			int NegativeCounter = -10;
			
			//add elements
			//if clusterID = 0, this is really probably unique, treat all cluster == 0 as unique sets.
			for (GenomicElementAndQueryMatch E: O1){
				if (E.getE().getClusterID() == 0){
					NegativeCounter--;
					O1Values.add(NegativeCounter);
				} else {
					O1Values.add(E.getE().getClusterID());
				}

			}
			
			for (GenomicElementAndQueryMatch E: O2){
				if (E.getE().getClusterID() == 0){
					NegativeCounter--;
					O2Values.add(NegativeCounter);
				} else {
					O2Values.add(E.getE().getClusterID());
				}
			}
			
			//Initialize values
			double Dissimilarity = 0;
			double NumIntersecting = 0;
			double SizeO1;
			double SizeO2;
			double SizeUnion = 0;
			
			//Hash Sets
			HashSet<Object> O1Hash = new HashSet<Object>(O1Values);
			HashSet<Object> O2Hash = new HashSet<Object>(O2Values);
			HashSet<Object> IntersectionHash = new HashSet<Object>(O1Values);
			HashSet<Object> UnionHash = new HashSet<Object>(O1Values);
			IntersectionHash.retainAll(O2Hash);
			UnionHash.addAll(O2Hash);
			
			SizeO1 = O1.size();
			SizeO2 = O2.size();

			//Find all intersecting types, and find the number that intersect.
			for (Object O : IntersectionHash){
				NumIntersecting = NumIntersecting + Math.min(Collections.frequency(O1Values, O), Collections.frequency(O2Values, O));
			}
			
			//compute union
			SizeUnion = SizeO1 + SizeO2 - NumIntersecting;

			if (!((SizeO1 == 0) && (SizeO2 == 0))){
				Dissimilarity = 1-(2*NumIntersecting)/(SizeO1+SizeO2);
			} else { //divide by zero case
				Dissimilarity = 0;
			}
			
			//Dice Measure
			return Dissimilarity;
			
			}
		}