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I can understand patenting things like file formats

The trouble with this is that file formats (and other communications protocols) have network effects, which greatly amplify the power granted to the patent holder.

>I can understand patenting things like file formats (e.g.: PSD) but general computer operation "controlling tones over a device connected to telephone lines to initiate a connection between a remote computer and a local one"

The former is a format. The latter sounds like a protocol. Formats should be patentable but protocols shouldn't?

I'm sure thankful all the Internet protocols weren't patented.

And I'm sure thankful formats like HTML aren't patented.

What's the difference between a file format and an API? I'm referencing the Oracle Java/Google Android API case.

I think it's not the file format itself, but the operations it takes to manipulate / transform data to get it into that format.

Patenting file formats make no sense to me. They are serializations of data, and although it can be convoluted how best to store a given representation of data the component parts must fall within mathematics.