You will probably need to use .getItemCount(slot) inside a loop and save that to a table, then check how much each has changed per update, however the problem arises when taking into account the removal of items.
How are you moving items out of the turtle?
Also, you could have the turtle put all the cobble into a chest, so it's inventory is empty. Then on the next update use the loop to check how much cobble it has and then empty the inventory again and repeat.
Edit: When using a loop to get the item count then dumping the items into a chest, you should take note of how fast the turtle inventory is filling up, just so you can optimize the program.
Ex: If your generator is only filling up slot 1 and maybe slot 2, just have it check the first 2 or 3 slots, no need to check all 16 each time.
Edited by Quintuple Agent, 14 February 2015 - 11:27 PM.