Refactoring phase III - succinctly rewriting functions towards a better OO design

[kwhitehall]

This is an umbrella issue related to refactoring phase stage III

Some guidelines:

1. If it is determined that a function is not used through the code base, then for now move the function to the bottom of the file and comment it out under a heading deprecated.
   In the next refactoring round, if we realize that there really is no need for them we'll remove those deprecated functions from the code base
2. If in rewriting, it is noticed that a function or sub-function will be better placed in another file based on the functionality, please feel free to do so.
   The current files functionality are:
   mccSearch.py - functions related to the actual detection algorithm
   iomethods.py - functions related to reading and writing files
   metrics.py - functions related to analyzing the detection
   plotting.py - functions related to making plots associated with metrics calculations or plot associated with the detection algorithm
   utils.py - functions that support the overarching task of mcs detection
   mccSearchUI.py - a CLI to complete a basic detection (for demo purposes)
3. Where useful and possible, please provide unittests for functions in the appropriate file in the test/ folder
   e.g. test/test_utils.py will contain unittests for functions in the utils.py
4. Please mention in the PR that the work is related to this issue.
5. Comment on this issue with other problems that you encountered during this phase and the solution (for consistency)