#' @include main.R
#' @include features-optimize.R
NULL
featuresOptimizerOpenMS <- setRefClass("featuresOptimizerOpenMS", contains = "featuresOptimizer")
featuresOptimizerOpenMS$methods(
checkInitialParams = function(params)
{
if (isoIdent != "OpenMS")
{
warning("Isotopic detection during feature finding will be disabled (by setting localMZRange=0). Set isoIdent=\"OpenMS\" to avoid this (see ?optimizeFeatureFinding).")
params[["localMZRange"]] <- 0
}
return(params)
},
fixDesignParam = function(param, value) if (param == "traceTermOutliers") round(value) else value,
fixOptParamBounds = function(param, bounds)
{
if (param == "traceTermOutliers")
return(round(bounds, 0))
return(bounds)
},
fixOptParams = function(params)
{
return(fixOptParamRange(params, list(c("minFWHM", "maxFWHM"),
c("minTraceLength", "maxTraceLength"))))
},
calculateResponse = function(params, task, keepObject)
{
# disable (excessive) logging and parallelization if necessary
opts <- list(patRoon.MP.logPath = FALSE)
if (parallel)
opts[c("patRoon.MP.method", "patRoon.MP.maxProcs")] <- list("classic", 1)
withr::with_options(opts, callSuper(params, task, keepObject))
}
)
generateFeatureOptPSetOpenMS <- function(...)
{
return(list(chromFWHM = c(5, 10),
mzPPM = c(3, 10),
minFWHM = c(1, 6),
maxFWHM = c(20, 40)))
}
getDefFeaturesOptParamRangesOpenMS <- function(params) list(localMZRange = c(0.00001, Inf),
traceTermOutliers = c(1, Inf))
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