Update plotSpectra environment to allow addFragments returned list

[guideflandre]

This PR is linked to this PSMatch issue and the discussed topics in #346

The motivation for this PR:

1. addFragments used to throw an error when multiple spectra where called
2. The new variable_modifications parameter necessitated a new addFragments function to distinguish annotations

The solution:
addFragments now returns a list of named elements (peptide sequence that includes modifications) containing a character() vector with the annotations. Each element of the list has an attribute linking the annotations to the spectrum it belonged to. In Spectra, the changes are located at the level of the presence of labels. It is assumed that most often than not, addFragments is called for labels. A quick check for variable modifications is also added (as plotSpectra doesn't support them yet). All three functions (plotSpectra, plotSpectraMirror and plotSpectraOverlay now support the version of addFragments in this PR).

This PR can only be accepted if the corresponding PR in PSMatch is accepted !! Otherwise, plotSpectra won't work.

[jorainer]

Thanks for the PR! I have however some questions.

[jorainer]

General comment: I don't know your specific use case, but would it not be possible to add whatever information/annotation you have or calculate directly to the Spectra object (as peaks or spectra variables) before plotting and then have a labels() function that can extract that information (or that even calculates it on the fly)? that was also the initial idea of accepting a function with parameter labels.

[guideflandre]

General comment: I don't know your specific use case, but would it not be possible to add whatever information/annotation you have or calculate directly to the Spectra object (as peaks or spectra variables) before plotting and then have a labels() function that can extract that information (or that even calculates it on the fly)? that was also the initial idea of accepting a function with parameter labels.

I believe we could if the number of annotations don't exceed length(x). In my use case, with variable modifications, I would have multiple annotations/spectrum which is not ideal.

[guideflandre]

A discussion with Laurent led to a potential different idea: the creation of a package specifically for plotting spectra. I understand my use cases might not fit in well within the plotSpectra environment, and it might need its separate function/package. I believe this should be an option/discussed too.

[lgatto]

@jorainer - we need to move on with this issue to be able to merge the new PSMatch functionality. Do we need another discussion.