Re-implement old features

[joewandy]

After code-refactoring, the following features are no longer supported in the simulated mass spec. They should be re-implemented at some point:

• Being able to define multiple isolation windows for one MS2 scan, see here. Also some unit tests for this have been commented out, make sure to uncomment them.
• Functional chromatograms only support Gaussian shapes, not gamma or uniform as before, see here.