Handling files without any spectra

[lgatto]

This issue deals with the problem described here, when a files doesn't contain any data (such as files containing only chromatographic data). If have done some small changes to deal with this:

> x <- readMSData(f0, mode = "onDisk")
Warning message:
In readOnDiskMSData(files = files, pdata = pdata, msLevel. = msLevel.,  :
  No spectra in file 'Lipidyzer Batch - 20151021124234 - 1 - 1-22766 - QC-05840.mzml'.
> x
MSn experiment data ("OnDiskMSnExp")
- - - Processing information - - -
Data loaded [Tue May 15 16:05:17 2018] 
 MSnbase version: 2.7.0 

But there's an issue when reading multiple files when one or more are empty of any spectra:

> readMSData(c(f0, msdata::proteomics(full.names = TRUE)[3]), mode = "onDisk")
Error in validObject(.Object) : 
  invalid class “OnDiskMSnExp” object: Spectra file indices in assayData does not match files in processinData.
In addition: Warning message:
In readOnDiskMSData(files = files, pdata = pdata, msLevel. = msLevel.,  :
  No spectra in file 'Lipidyzer Batch - 20151021124234 - 1 - 1-22766 - QC-05840.mzml'.

The error above happens because there are 2 file names in the processingData slots, but only one in the assayData/featureData. This is expected, but how should we deal with this?

• Remove that check from the validity method - I would prefer not do this.
• Keep track of empty files and keep this into account in the validity method - this will increase complexity of the code base for a edge case.
• Do not consider these file names in the processingData at all. The user will know about this as a warning is returned when reading the file, but there won't be any trace later on (unless we log this) - my preferred fix.

@sgibb @jotsetung - any opinion or suggestion?

[jorainer]

I'd suggest to implement a low level hasSpectra and hasChromatograms function (eventually in mzR). This could be used to guide the user also to other function to read data (e.g. if a file does not contain spectra, but only chromatograms and the user wants to read that using readMSData the error message could suggest to use the readSRMData instead).