Support OR

[jorainer]

Support an OR for matching values (as described in here).
Specifically, we want to support queries such as WHERE MS2PROD=(100 OR 104):TOLERANCEPPM=5. This should ideally work for all conditions, e.g. also for MS2PREC etc.

[andreavicini]

The functions .translate_filter_ms2prec and .translate_filter_ms2nl use filter functions from Spectra: filterPrecursorMzand containsNeutralLoss which allow only one value (of mz or neutral loss). Assuming we have
a query like WHERE MS2PREC=(100 OR 104):TOLERANCEPPM=5 we would need to check both values (100 and 104).
At the moment .translate_filter_ms2prec returns ProcessingStep(filterPrecursorMz, ARGS = list(mz = mzr)) which is ok if mzr has length 1. Maybe to solve the problem at the origin one could modify the filterPrecursorMz so that it receives also vectors. Otherwise I was thinking to define a filter function like

filt_fun <- function(x, pmz, tolerance, ppm) { mzr <- pmz + c(-1, 1) * (tolerance + ppm(pmz, ppm = ppm)) do.call(c, lapply(mzr, function(v) ProcessingStep(filterPrecursorMz, ARGS = list(mz = v)))) }

and return ProcessingStep(filt_fun, ARGS = list(pmz, tolerance, ppm)). This however can have problems because due to tolerance and ppm different calls to filterPrecursorMz could return the same spectra leading to duplicates in the final spectra returned.

[jorainer]

Good point. I will have a look into the filterPrecursorMz function in Spectra.