Getting closer to a subanalysis mode

Getting closer to a subanalysis mode
This is a big patch, in order to create the subanalysis mode I wanted a
class that'd hold a reference to a sequence and some start/stop locations
which'd let the user edit what region they want to use in the subanalysis
before creating the new analysis.

I started setting up a SequenceLocation and SequenceLocationModel (for
the qt MVC classes) but then I learned that C++ reference types aren't
particularly good things to store in containers, as when the original
variable that all the references are pointing to goes away you get
invalid memory exceptions.

So I went through and switched most of those references to the
boost::shared_ptr which is a fairly simple reference counted pointer.

This did make most of the C++ code happy, but my python wrapping
is increasingly losing functionality.

Also as a bonus this increased use of pointers I think will improve the
sharing of the AnnotationColors color mappers.