Pass settings object to initAnalysis().

Pass settings object to initAnalysis().

Makes it easier to write analysis modules that need to access some
settings based on user input, and is also prerequisite for issue #839.
With the settings object, it is possible to pass additional information
to this method without changing the signature, simplifying maintenance.
In an earlier design, the settings object was available in all methods
through a separate accessor method, but the availability of the settings
became too restricted when this was refactored to make
TrajectoryAnalysisModule more interface-like.

Change-Id: If775db348354b6ba35c6d7cb0a10fe5057b6e1b2