eicWorkflow: added fragment eic retrieval

R/eicWorkflow.R

@@ -25,6 +25,29 @@ eicWorkflow <- function(
       as("SimpleList")
     do.call(progressbar, list(object=pb, close=TRUE))
   }
+
+  # Step 2: acquire EIC for fragments from files
+  if(2 %in% steps)
+  {
+
+    rmb_log_info("eicWorkflow: Step 2. Acquire fragment 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, 
+                  extractCpdFragmentEics, 
+                  mode=mode, 
+                  ppm=settings$findMsMsRawSettings$ppmFine,
+                  precursor_dmz = settings$findMsMsRawSettings$mzCoarse,
+                  rt_window = settings$rtMargin,
+                  progressbar = list(hook=progressbar, pb=pb)
+      ) |>
+      as("SimpleList")
+    do.call(progressbar, list(object=pb, close=TRUE))
+  }
+
   w
 
 }
@@ -46,10 +69,89 @@ extractCpdParentEic <- function(cpd, file, mode, ppm, progressbar = NULL) {
   return(cpd)
 }
 
-extractCpdFragmentEics <- function(cpd) {
+
+.fixHeaderData  <- function(headerData) {
+
+  headerData$precursorScanNum <- NA
+  headerData[which(headerData$msLevel == 1),"precursorScanNum"] <-
+    headerData[which(headerData$msLevel == 1),"acquisitionNum"]
+  headerData[,"precursorScanNum"] <- RMassBank:::.locf(headerData[,"precursorScanNum"])
+  # Clear the actual MS1 precursor scan number again
+  headerData[which(headerData$msLevel == 1),"precursorScanNum"] <- 0
+  # Remove precursors which are still NA in precursor scan num.
+  # This removes a bug when filling precursor if the first scan(s) are MS2 before a
+  # MS1 scan appears. The resulting NA values in precursorScanNum are problematic downstream.
+  headerData <- headerData[!is.na(headerData$precursorScanNum),]
+
+  return(headerData)
+}
+
+extractCpdFragmentEics <- function(cpd, file, mode, 
+                                   ppm, precursor_dmz, rt_window,
+                                   progressbar = NULL) {
 
+  attr(cpd, "file") <- file
+
+  d <- mzR::openMSfile(file)
+  h <- mzR::header(d)
+  p <- RMassBank::makePeaksCache(d, h)
+
+  # 1.6.22: For Exploris data, we need to fill precursor here.
+  h <- .fixHeaderData(h)
+
+  if(length(cpd@children) == 0)
+    return(cpd)
+
+  if(!cpd@found)
+    return(cpd)
+
+  cpd@children <- cpd@children |>
+    as.list() |>
+    purrr::map(extractSpectrumFragmentEics,
+        header = h, peaksCache = p,
+        ppm=ppm, precursor_dmz=precursor_dmz, rt_window=rt_window * 60) |>
+    as("SimpleList")
+
+
+
+
+  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)
 }
 
-extractSpectrumFragmentEics <- function(cpd, sp) {
+extractSpectrumFragmentEics <- function(
+    sp, header, peaksCache,
+    ppm, precursor_dmz, rt_window) {
+  hSub <- header |> dplyr::filter(
+    abs(precursorMZ - sp@precursorMz) < precursor_dmz,
+    msLevel == sp@msLevel,
+    polarity == sp@polarity,
+    abs(retentionTime - sp@rt) < rt_window,
+    collisionEnergy == sp@collisionEnergy
+  )
+  if(nrow(hSub) == 0)
+  {
+    attr(sp, "eics") <- list()
+    return(sp)
+  }
+  hSub$msLevel <- 1
+  pSub <- peaksCache[hSub$seqNum]
+
+  mzs <- sp@mz
+  if(!is.null(RMassBank::property(sp, "mzRaw")))
+    mzs <- RMassBank::property(sp, "mzRaw")
+
+  eics <- lapply(mzs, function(mz) {
+    eic <- RMassBank::findEIC(d, mz, RMassBank::ppm(mz, ppm, p = TRUE), headerCache = hSub, peaksCache = pSub)
+    eic$precursorScan <- hSub$precursorScanNum
+    eic$mz <- mz
+    eic
+  })
 
+  attr(sp, "eics") <- eics
+  return(sp)
 }