--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fun/ProbShared2.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,75 @@
+package fun;
+
+import java.util.HashSet;
+import java.util.Random;
+
+import dna.AminoAcid;
+
+public class ProbShared2 {
+
+	public static void main(String args[]){
+		int k=Integer.parseInt(args[0]);
+		int len1=Integer.parseInt(args[1]);
+		int len2=Integer.parseInt(args[2]);
+		int rounds=Integer.parseInt(args[3]);
+		
+		System.out.println("Probability:   "+simulate(k, len1, len2, rounds));
+	}
+	
+	static double simulate(int k, int len1, int len2, int rounds){
+		int successes=0;
+		final HashSet<Long> set=new HashSet<Long>();
+		for(int i=0; i<rounds; i++){
+			successes+=simulateOnePair(k, len1, len2, set);
+		}
+		return successes/(double)rounds;
+	}
+	
+	static int simulateOnePair(int k, int len1, int len2, HashSet<Long> set){
+		set.clear();
+		
+		final int shift=2*k;
+		final long mask=(shift>63 ? -1L : ~((-1L)<<shift));
+		long kmer=0;
+		int len=0;
+		
+		byte[] bases=randomSequence(len2);
+		
+		for(int i=0; i<bases.length; i++){
+			byte b=bases[i];
+			long x=baseToNumber[b];
+			kmer=((kmer<<2)|x)&mask;
+			if(x<0){len=0;}else{len++;}
+			if(len>=k){
+				set.add(kmer);
+			}
+		}
+		
+		bases=randomSequence(len1);
+		
+		for(int i=0; i<bases.length; i++){
+			byte b=bases[i];
+			long x=baseToNumber[b];
+			kmer=((kmer<<2)|x)&mask;
+			if(x<0){len=0;}else{len++;}
+			if(len>=k){
+				if(set.contains(kmer)){return 1;}
+			}
+		}
+		return 0;
+	}
+	
+	static byte[] randomSequence(int len){
+		byte[] array=new byte[len];
+		for(int i=0; i<len; i++){
+			int number=randy.nextInt(4);
+			array[i]=AminoAcid.numberToBase[number];
+		}
+		return array;
+	}
+	
+	static final Random randy=new Random();
+	static final byte[] numberToBase=AminoAcid.numberToBase;
+	static final byte[] baseToNumber=AminoAcid.baseToNumber;
+	
+}