Optimizing my game

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... and, I believe, JGOware was stating that you're more likely to get a performance issue transferring data to the GPU than using the CPU.
With that in mind :
Have you timed your code without drawing anything?
What is the difference between the maths+draw vs the draw? Simply time your update logic and not your draw logic.
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Another point, you haven't given much to go on so people are guessing things that might help.
Your original question concerned the overhead for calling functions/methods (even 1000's of times). A quick test on my machine suggested using methods adds 1ms per 10000 calls.
I understand the argument that every ms counts but I doubt that will make a slow framerate into an acceptable framerate.