Refs #9170 More refactoring and tidying

The merged changes have been updated to be consistant in terms of connections and naming conventions

White space has been imporved

Existing docstrings have been updated to double quotes rather than single and have been moved to the proper place below Def. Some docstrings have been changed to comments

Some initialisations have been moved to the constructor
Refs #9170 Added Docstrings to all methods

All methods now have a docstring in the right place