Beginnings of classes

Started work in refactoring code to classes.
Update of the rates class

First transmission matrix should be 0.1 not 1.
Class and Header files.

Basic compiling version working. Needs final tweaks on thursday for a
full simulation.
Refactoring complete

Class version all done. Final version under current code.
Merge pull request #17 from MattDeanMPhys/DeansRefactoring

Deans refactoring