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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;
}
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