Removed a bunch of unused local variables (PMD reports)

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed an unnecessary Integer instantiation in a boolean test.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Moved IAtomColorer from the interfaces to the render module

Change-Id: Ie560b864f0123a848fe160da627b3d8d058984ee
Signed-off-by: John May <john.wilkinsonmay@gmail.com>