I had to change the algorithm with java. Instead of the standard rook and bishop move generation, I split 
them up into directions and then get each direction individually. This is slower but stops me needing a 64x4096 and
64x512 array. This exceeds the max size for a class, so I went with this approach.

I finally got java to work after loads of trial and error. Having to use signed longs can cause many problems in certain situations.
Like in bitScanForward.