It's a METHOD of doing something. You can view each step of the method as a little black box with an input from the previous step and an output to the next. It is irrelevant TO THE METHOD what is in each black box. It could be some hardware, it could be software, it could be a little fairy with a wand and some fairy dust. It doesn't matter. What matters is whether the method - as a series of technical steps - is novel and inventive.
Maybe the method steps are not actually novel or lack an inventive step, I don't know as I've not studied the patent and related prior art and I don't intend to, it's not my field of work. I can only assume my colleagues did a thorough job and found that the method being claimed was both novel and inventive. Implementing something in a computer or with software when that is the only difference to the prior art is not patentable under the EPC as lacking (amongst other things) inventive step. This is very clear if you understand European Patent Law. There must therefore have been, in the eyes of the examiners, something inventive in the particular series of method steps as claimed in the granted patent specification. The parts of the independent claims referring to computer implementation will not have formed part of that reasoning. Furthermore, the general public (and ALL of Apple's competitors) had years in which they could oppose and comment on the application before it was granted and nobody did.
I refer you back to my point - please learn some patent law before commenting on these cases. Yes, I've been around here a while and yes I know that most people comment on stuff here without reading the stories and without actually having any knowledge of the subject in question. I can usually resist but when people are choosing to mock my chosen career and the work carried out by my colleagues in the EPO, without any form of knowledge or study to back-up their obviously idiotic bias, it annoys me a tad.