Factored out transition building
Got rid of a special case in the transition matrix computations
Replaced for loops and explicit sums with a linear algebra expression

It might be less clear to read, but there are fewer local variables and loops in the code now and that is good. Plus, with scipy I think this code should also be a lot faster.
Moved the general transition code to its own module and added a class for parsing information to it.
Renamed state sets
Merge branch 'feature/cleaner_transition_computations' into develop