Using a BitSet object

Question

Hello !
I would like to store into MySQL a BitSet object. I am able to only use a string to do that :BitSet subBS = new BitSet();
String strSubSet = "";
subBS = Fingerprinter.getFingerprint(mol, 2048, 6);
strSubSet = subBS.toString();This string could be verry big comparred to the object itself (more than 5 ko).
Is it possible to be more efficient to store this BitSet into MySQL ?
Thank you for your help,
Jean-Marie

Answer 1

public class RLE {
    public static String compress(BitSet bs) {
        boolean state = bs.get(0);
        int count = 0, l = bs.size();
        String ret = Integer.toString(l, Character.MAX_RADIX) + "," + (state ? "1" : "0");
        for(int i = 0; i < l; i++) {
            if(bs.get(i) == state){
                count++;
            }else{
                ret += "," + Integer.toString(count, Character.MAX_RADIX);
                count = 1;
                state = !state;
        return ret + "," + Integer.toString(count, Character.MAX_RADIX);
    public static BitSet expand(String s) {
        BitSet ret = new BitSet(Integer.valueOf(a[0], Character.MAX_RADIX));
        String[] a = s.split(",");
        boolean state = a[1].equals("1");
        int idx = 0, t;
        for(int i = 2; i < a.length; i++) {
            t = Integer.valueOf(a, Character.MAX_RADIX);
if(state)
ret.set(idx, idx + t);
idx += t;
state = !state;
return ret;
So you can store your BitSet using [i]RLE.compress(subBS) then retrieve it later using RLE.expand(strSubSet).
Hope this helps~
Alex Lam S.L.