jpayne@68: package fun;
jpayne@68: 
jpayne@68: public class ProbShared {
jpayne@68: 
jpayne@68: 	public static void main(String args[]){
jpayne@68: 		int k=Integer.parseInt(args[0]);
jpayne@68: 		int len1=Integer.parseInt(args[1]);
jpayne@68: 		int len2=Integer.parseInt(args[2]);
jpayne@68: 
jpayne@68: 		System.out.println("Cardinality 1: "+cardinality(k, len1));
jpayne@68: 		System.out.println("Cardinality 2: "+cardinality(k, len2));
jpayne@68: 		System.out.println("Probability:   "+probIntersect(k, len1, len2));
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	static int cardinality(int k, int seqLength){
jpayne@68: 		double space=Math.pow(4, k);
jpayne@68: 		int kmers=seqLength-k+1;
jpayne@68: 		double unique=0;
jpayne@68: 		for(int i=0; i<kmers; i++){
jpayne@68: 			double prob=(space-unique)/space;
jpayne@68: 			unique+=prob;
jpayne@68: 		}
jpayne@68: 		return (int)Math.round(unique);
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	static double probIntersect(int k, int len1, int len2){
jpayne@68: 		int card1=cardinality(k, len1);
jpayne@68: 		int card2=cardinality(k, len2);
jpayne@68: 		double space=Math.pow(4, k);
jpayne@68: 		double cumulativeProbUnshared=1;
jpayne@68: 		for(int i=0; i<card1; i++){
jpayne@68: 			double probShared=card2/space;
jpayne@68: 			double probUnshared=1-probShared;
jpayne@68: 			space-=probUnshared;
jpayne@68: 			cumulativeProbUnshared*=probUnshared;
jpayne@68: 		}
jpayne@68: 		return 1-cumulativeProbUnshared;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: }