Hope this helps. But: 1) I'm a CS/Math Major, but I don't speak perl (yet). 2) I only spent like 10 minuts on this. 3) I havn't even tried to compile this. Summary) Here's a nice non-recursive algorithm, but I won't vouch for the code. ;) It should take the @ControlMatrix and produce a 3 dimensional array @perms that looks something like this: 
@ControlMatrix = ( [1, 2, 0, 2], [0, 0, 2, 1] )
@perms = (
  ([1, 0, 0, 0], [1, 1, 0, 0], [1, 0, 0, 1], [1, 1, 0, 1])
  ([0, 0, 0, 1], [1, 1, 1, 1])
)

[download]
Here's my guess: 
$index = 0;
$pcount = 1;

for ($names = 0; $names < @ControlNames.length; $names++) {
  for ($fields = 0; $fields < $ControlMatrix[$names].length; $fields++
+) {
    if (@ControlMatrix[$names][$fields] < 2 ) {
      for ($q = 0; $q < $pcount; $q++) {
        @perms[$names][$q][$fields] = @ControlMatrix[$names][$fields];
      }
    } else {
      for ($q = 0; $q < $pcount; $q++) {
        @perms[$names][$q+$pcount] = @perms[names][$q];
        $perms[$names][$q][$fields] = 0;
        $perms[$names][$q+$pcount][$fields] = 1;
      }
      $pcount *= 2;
    }
  }
}

[download]

In reply to Re: Permutation algorithm? by Lexicon
in thread Permutation algorithm? by Shayk

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