Chemical Reactions (solution) Java

import java.io.*;
import java.util.*;

public class Main {

    public static void main(String[] args) throws IOException{

        class Reaction {
            ArrayList<Integer> in = new ArrayList<Integer>(), out = new ArrayList<Integer>();
            Reaction(String s)
            {
                int number = 0, base = 1, middle = s.length()-1;
                for (int j = s.length()-1; j >= 0; j--) {
                    char c = s.charAt(j);
                    if (c >= '0' && c <= '9')
                    {
                        number += (c - '0') * base; base *= 10;
                    }
                    else {
                        base = 1;
                        out.add(number);
                        number = 0;
                    }
                    if (c == '>')
                    {
                        middle = j - 2;
                        break;
                    }

                }
                for (int j = middle; j >= 0; j--) {
                    char c = s.charAt(j);
                    if (c >= '0' && c <= '9')
                    {
                        number += (c - '0') * base;
                        base *= 10;
                    }
                    else {
                        base = 1;
                        in.add(number);
                        number = 0;
                    }
                    if (j == 0)
                    {
                        in.add(number);
                        break;
                    }
                }
            }
            @Override
            public String toString()
            {
                return in.toString() + "->" + out.toString();
            }
        }

        Date current = new Date();
        Date start = current;
        BufferedReader bi = new BufferedReader(new InputStreamReader(System.in));

        String chemicals_string = bi.readLine();
        HashSet<Integer> chemicals = new HashSet<Integer>();

        int number = 0, base = 1;
        for (int j = chemicals_string.length()-1; j >= 0; j--) {
            char c = chemicals_string.charAt(j);
            if (c >= '0' && c <= '9')
            {
                number += (c - '0') * base; base *= 10;
            }
            else {
                base = 1;
                chemicals.add(number);
                number = 0;
            }
            if (j == 0)
            {
                chemicals.add(number);
                break;
            }

        }
        //System.out.println("Reading chemicals takes: " + (new Date().getTime() - current.getTime()) + " ms");

        ArrayList rlist = new ArrayList(100000);
        String line;
        current = new Date();
        while ((line = bi.readLine()) != null)
        {
            rlist.add( new Reaction(line));
        }

        //System.out.println("Reading react takes: " + (new Date().getTime() - current.getTime()) + " ms and ");
        //System.exit(0);
        current = new Date();
        boolean newchemicalsfound = true;
        int counter = 0;
        while (newchemicalsfound)
        {
            counter++;
            newchemicalsfound = false;
            for(Iterator<Reaction> i = rlist.iterator(); i.hasNext(); )
            {
                Reaction r = i.next();
                if (chemicals.containsAll(r.in))
                {
                    chemicals.addAll(r.out);
                    i.remove();
                    newchemicalsfound = true;
                }
            }

        }
        //System.out.println("loop takes: " + (new Date().getTime() - current.getTime()) + " ms and " + counter + "steps");
        current = new Date();
        StringBuilder output = new StringBuilder();
        for (Integer c : chemicals)
        {
            output.append(c);
            output.append(" ");
        }
        //System.out.println("Building string takes: " + (new Date().getTime() - current.getTime()) + " ms");

        BufferedWriter out = new BufferedWriter(new OutputStreamWriter(System.out));
        out.write(output.toString()); out.flush();
        //System.out.println(output);
        //System.out.println("Total time: " + (new Date().getTime() - start.getTime()) + " ms");
    }
}