Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fun/Genetic.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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67:0e9998148a16 68:5028fdace37b
1 package fun;
2
3 import java.util.Arrays;
4 import java.util.Random;
5
6 public class Genetic {
7
8 public static void main(String[] args){
9 Genetic g=new Genetic(args);
10 long answer=g.solve();
11 System.out.println(Long.toBinaryString(answer)+" \t-> "+f(answer));
12 }
13
14 public Genetic(String[] args){
15 pop=(args.length>0 ? Integer.parseInt(args[0]) : 20);
16 bits=(args.length>1 ? Integer.parseInt(args[1]) : 8);
17 iters=(args.length>2 ? Integer.parseInt(args[2]) : 20);
18 mutProb=(args.length>3 ? Double.parseDouble(args[3]) : 0.01);
19 mask=(bits>63 ? -1L : ~((-1L)<<bits));
20 }
21
22 public long solve(){
23 final long mask=(bits>63 ? -1L : ~((-1L)<<bits));
24 double[] prob=new double[pop];
25 Bug[] current=new Bug[pop];
26 for(int i=0; i<pop; i++){
27 current[i]=new Bug(randy.nextLong()&mask);
28 }
29 Arrays.sort(current);
30 Bug best=current[current.length-1];
31
32 for(int i=0; i<iters; i++){
33
34 if(true){
35 System.out.println("Iteration "+i+": "+current[current.length-1]);
36 }
37
38 current=iterate(current, prob);
39 Arrays.sort(current);
40 if(best.compareTo(current[current.length-1])<0){best=current[current.length-1];}
41 }
42
43 return best.dna;
44 }
45
46 public Bug[] iterate(Bug[] current, double[] prob){
47 Arrays.fill(prob, 0);
48 double sum=0;
49 for(int i=0; i<current.length; i++){
50 Bug b=current[i];
51 sum+=b.fitness;
52 prob[i]=b.fitness;
53 }
54 double mult=1/sum;
55 prob[0]*=mult;
56
57 for(int i=1; i<prob.length; i++){
58 prob[i]=prob[i-1]+prob[i]*mult;
59 }
60
61 Bug[] next=new Bug[current.length];
62 for(int i=0; i<next.length; i++){
63 long babyDna=breed(current, prob, mutProb);
64 next[i]=new Bug(babyDna);
65 }
66 return next;
67 }
68
69 public long breed(Bug[] current, double[] prob, double mutProb){
70 double fa=randy.nextDouble();
71 double fb=randy.nextDouble();
72 Bug a=current[findIndex(fa, prob)];
73 Bug b=current[findIndex(fb, prob)];
74 long crossover=randy.nextLong();
75 long baby=(a.dna&crossover)|(b.dna&~crossover);
76 if(mutProb>0 && randy.nextDouble()<mutProb){
77 long bit=(1L<<randy.nextInt(bits));
78 baby^=bit;
79 }
80 return baby;
81 }
82
83 public int findIndex(double f, double[] prob){
84 for(int i=pop-1; i>0; i--){
85 if(prob[i-1]<f){return i;}
86 }
87 return 0;
88 }
89
90 public static double f(long x){
91 return x*x;
92 }
93
94 private static class Bug implements Comparable<Bug> {
95
96 public Bug(long dna_){
97 dna=dna_;
98 fitness=f(dna);
99 }
100
101 @Override
102 public int compareTo(Bug b){
103 return (fitness<b.fitness ? -1 : fitness>b.fitness ? 1 : 0);
104 }
105
106 @Override
107 public String toString(){
108 return Long.toBinaryString(dna)+" \t-> "+fitness;
109 }
110
111 final long dna;
112 final double fitness;
113 }
114
115 public static final Random randy=new Random();
116
117 final int pop;
118 final int bits;
119 final int iters;
120 final double mutProb;
121
122 final long mask;
123
124 }