I had to change the algorithm with java. Instead of the standard rook and bishop knight move generation, I split 
them up into direction and then get each direction individually. This is slower but stops me need a 54x4096 and
64x512 array. This is a problem because ulongs are directly supported in java.

You have two choices
1. convert all the constants to minus if they are over the max a signed long and risk a lot of bugs and testing that way.
2. convert all the constants to BigIntegers like this:
     static final BigInteger MAX_ULONG = new BigInteger("18446744073709551615");
This means replacing all values with this type in all constants. You also need to use OOP for everything.
This:
    BigInteger bitboard = bitboard1 & bitboard2;
Turns into:
    BigInteger bitboard = bitboard1.and(bitboard2);

I chose the second approach and tried converting everything over to this. I created so many bugs that I couldn't fix and 
gave up in the end.