Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fun/ProbShared.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 package fun;
jpayne@68 2
jpayne@68 3 public class ProbShared {
jpayne@68 4
jpayne@68 5 public static void main(String args[]){
jpayne@68 6 int k=Integer.parseInt(args[0]);
jpayne@68 7 int len1=Integer.parseInt(args[1]);
jpayne@68 8 int len2=Integer.parseInt(args[2]);
jpayne@68 9
jpayne@68 10 System.out.println("Cardinality 1: "+cardinality(k, len1));
jpayne@68 11 System.out.println("Cardinality 2: "+cardinality(k, len2));
jpayne@68 12 System.out.println("Probability: "+probIntersect(k, len1, len2));
jpayne@68 13
jpayne@68 14 }
jpayne@68 15
jpayne@68 16 static int cardinality(int k, int seqLength){
jpayne@68 17 double space=Math.pow(4, k);
jpayne@68 18 int kmers=seqLength-k+1;
jpayne@68 19 double unique=0;
jpayne@68 20 for(int i=0; i<kmers; i++){
jpayne@68 21 double prob=(space-unique)/space;
jpayne@68 22 unique+=prob;
jpayne@68 23 }
jpayne@68 24 return (int)Math.round(unique);
jpayne@68 25 }
jpayne@68 26
jpayne@68 27 static double probIntersect(int k, int len1, int len2){
jpayne@68 28 int card1=cardinality(k, len1);
jpayne@68 29 int card2=cardinality(k, len2);
jpayne@68 30 double space=Math.pow(4, k);
jpayne@68 31 double cumulativeProbUnshared=1;
jpayne@68 32 for(int i=0; i<card1; i++){
jpayne@68 33 double probShared=card2/space;
jpayne@68 34 double probUnshared=1-probShared;
jpayne@68 35 space-=probUnshared;
jpayne@68 36 cumulativeProbUnshared*=probUnshared;
jpayne@68 37 }
jpayne@68 38 return 1-cumulativeProbUnshared;
jpayne@68 39 }
jpayne@68 40
jpayne@68 41 }