eicWorkflow step 1: added progress bar

R/eicWorkflow.R

@@ -1,33 +1,48 @@
 
 
-eicWorkflow <- function(w, mode="pH", steps=c(1:8),
-          settings = getOption("RMassBank")) {
+eicWorkflow <- function(
+    w, mode="pH", steps=c(1:8),
+    settings = getOption("RMassBank"),
+    progressbar = "progressBarHook"
+    ) {
 
   # Step 1: acquire EIC for parent from files
   if(1 %in% steps)
   {
+
     rmb_log_info("eicWorkflow: Step 1. Acquire parent EIC from files")
+    spectra_count <- length(w@spectra)
+    pb <- do.call(progressbar, 
+                  list(object=NULL, value=0, min=0, max=spectra_count))
+
     w@spectra <- w@spectra |> as.list() |>
       purrr::map2(w@files, 
                   extractCpdParentEic, 
                   mode=mode, 
-                  ppm=settings$filterSettings$ppmFine
+                  ppm=settings$findMsMsRawSettings$ppmFine,
+                  progressbar = list(hook=progressbar, pb=pb)
           ) |>
       as("SimpleList")
+    do.call(progressbar, list(object=pb, close=TRUE))
   }
   w
 
 }
 
 
-extractCpdParentEic <- function(cpd, file, mode, ppm) {
+extractCpdParentEic <- function(cpd, file, mode, ppm, progressbar = NULL) {
 
   d <- mzR::openMSfile(file)
-  h <- header(d)
+  h <- mzR::header(d)
   h <- h[h$polarity == RMassBank:::getAdductPolarity(mode),]
-  mz <- findMz(cpd@id, mode = mode, ppm = ppm)
-  eic <- findEIC(d, mz, headerCache = h)
+  mz <- RMassBank::findMz(cpd@id, mode = mode, ppm = ppm)
+  eic <- RMassBank::findEIC(d, mz, headerCache = h)
   attr(cpd, "eic") <- eic
+  if(!is.null(progressbar)) {
+    value <- do.call(progressbar$hook, list(object=progressbar$pb, value=NULL))
+    do.call(progressbar$hook, list(object=progressbar$pb, value=value+1))
+  }
+
   return(cpd)
 }
 

R/leMsMs.r

@@ -2355,14 +2355,18 @@ recalibrate.linear <- function(rcdata)
 #' 
 #' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
 #' @export
-progressBarHook <- function(object = NULL, value = 0, min = 0, max = 100, close = FALSE)
+progressBarHook <- function(object = NULL, value = NULL, min = 0, max = 100, close = FALSE)
 {
 	if(is.null(object))
 	{
 		object <- txtProgressBar(min, max, value, style=3, file=stderr())
 	}
 	if(close)
 		close(object)
+  if(is.null(value))
+  {
+    return(getTxtProgressBar(object))
+  }
 	else
 	{
 		setTxtProgressBar(object, value)