public class CustomSort implements Comparator<IBlockState> {
    @Override
    public int compare(IBlockState arg0, IBlockState arg1) {
        return arg0.getBlock().toString().compareTo(arg1.getBlock().toString()); // Sort in alphebetical order.
    }
}

public class Generate implements IWorldGenerator {
    int Min = 0;
    int Max = 128;
    int Range = Max-Min+1;
    @Override
    public void generate(Random random, int chunkX, int chunkZ, World world, IChunkGenerator chunkGenerator,
            IChunkProvider chunkProvider) {
        // TODO Auto-generated method stub
        for (int X = 0; X < 16; X++)
        {
            for (int Z = 0; Z < 16; Z++)
            {
                IBlockState[] Main = new IBlockState[Range]; // Main array. (Sorry if I say table on accident anywhere, used to Lua)
                List<IBlockState> B = new ArrayList<IBlockState>(); // Array for sorting blocks, so we leave lava, water, and air where they are.
                for (int Y = Min; Y < Max; Y++) // Min and max were originally to test because I thought it would take hours to generate.
                {
                    Main[Y-Min] = chunkProvider.getLoadedChunk(chunkX, chunkZ).getBlockState(X, Y, Z); // Add the block to the array.
                }
                int Pos = 0;
                for (int I = 0; I < Range; I++) // Add blocks that are not water, lava, or air to the sorting array.
                {
                    // This next like is some ugly hard-coding, but I really am not up to doing anything about it for the time being.
                    if (Main[I] != null && Main[I].getBlock() != Blocks.AIR && Main[I].getBlock() != Blocks.WATER && Main[I].getBlock() != Blocks.LAVA)
                    {
                        B.add(Main[I]);
                        Pos++; // Increment the position only after we know that it is a valid sortable block.
                    }
                }
                Pos = 0;
                Collections.sort(B, new CustomSort()); // Sort it with the function above.
                for (int I = 0; I < Range; I++) // This loop puts the stuff back in the array Main.
                {
                    // This preserves the structure and shape of liquids and air.
                    if (Main[I] != null && Main[I].getBlock() != Blocks.AIR && Main[I].getBlock() != Blocks.WATER && Main[I].getBlock() != Blocks.LAVA) {
                        Main[I] = B.get(Pos);
                        Pos++;
                    }
                }
                for (int Y = Min; Y < Max; Y++)
                {
                    chunkProvider.getLoadedChunk(chunkX, chunkZ).setBlockState(new BlockPos(X, Y, Z), Main[Y-Min]); // Main contains IBlockStates, making this easy.
                }
            }
        }
    }
}