We plan to have 3 layers:
MSnbase- see respective packages.
The data to be plotted can have mixed origins. File access, in memory or a mix of both.
environmentfor easy access by the GUI component
The problem with the above is that the data is duplicated, which we don't want to do. Idea 2 would be something like a set of rules:
if the data is in a file, we access it through mzR like this ...
if the data is in an MSnExp instance, we access it like this ...
For a file access, rule 1 would be the default. For and
MSnExp access, rule 2 would be the default. For mixed access, we would create a set of spectra (their acquisition numbers for example) that access via rule 2, and all the other ones through disk access.
I suggest to start working on the file access only mode. If we restrict
MSnExp visualisation to cases where the raw file is present (*), we can more or less replace that case with the former.
(*) The file name can be obtained with
fileNames(), and we can verify that it is available with