injection time is now added by default in readMSData2

DESCRIPTION

@@ -63,6 +63,7 @@ Imports:
     lattice,
     ggplot2,
     S4Vectors,
+    XML,
     Rcpp
 Suggests:
     testthat,
@@ -85,7 +86,6 @@ Suggests:
     imputeLCMD,
     norm,
     gplots,
-    XML,
     shiny
 LinkingTo: Rcpp
 License: Artistic-2.0

NAMESPACE

@@ -12,6 +12,9 @@ import(impute)
 import(lattice)
 import(methods)
 
+importFrom(XML, xmlInternalTreeParse, getDefaultNamespace, xpathApply,
+           xmlAttrs)
+
 importFrom(graphics, abline, axis, grid, legend, lines, points, text,
            barplot, layout, par)
 importFrom(stats, ave, median, medpolish, quantile, reorder, setNames,
@@ -156,7 +159,6 @@ exportMethods(updateObject,
               "sampleNames<-",
               fileNames,
               msInfo,
-              isolationWindow,
               expemail, exptitle,
               ionSource, ionSourceDetails,
               analyser, analyzer,

R/AllGenerics.R

@@ -142,4 +142,3 @@ setGeneric("filterFile", function (object, ...) standardGeneric("filterFile"))
 setGeneric("filterAcquisitionNum", function (object, ...) standardGeneric("filterAcquisitionNum"))
 
 ## isolationWindow generic is in mzR
-setGeneric("addInjectionTime", function(object, ...) standardGeneric("addInjectionTime"))

R/header.R

@@ -0,0 +1,13 @@
+## These data should eventually be extracted in mzR and added to the
+## default header
+
+injectionTimeFromFile1 <- function(f) {
+    xvals <- vector("list", length = length(f))
+    doc <- XML::xmlInternalTreeParse(f)
+    namespaceDef <- XML::getDefaultNamespace(doc)
+    ns <- c(x = namespaceDef[[1]]$uri)
+    x <- XML::xpathApply(doc, "//x:cvParam[@accession = 'MS:1000927']",
+                         namespaces = ns, xmlAttrs)
+    xvals <- sapply(x, "[", "value")
+    as.numeric(unlist(xvals))
+}

R/methods-MSnExp.R

@@ -344,39 +344,3 @@ setMethod("isolationWindow", "MSnExp",
               ## TODO - add to fData
               mzR::isolationWindow(fileNames(object), ...)
           })
-
-setMethod("addInjectionTime", "MSnExp",
-          function(object, ...) {
-              stopifnot(requireNamespace("XML"))
-              if ("injectionTime" %in% fvarLabels(object))
-                  stop("injectionTime feature variable already present.")
-              f <- fileNames(object)
-              xvals <- vector("list", length = length(f))
-              for (i in seq_along(f)) {
-                  obj <- filterFile(object, i)
-                  doc <- xmlInternalTreeParse(fileNames(obj))
-                  namespaceDef <- getDefaultNamespace(doc)
-                  ns <- c(x = namespaceDef[[1]]$uri)
-                  x <- xpathApply(doc, "//x:cvParam[@accession = 'MS:1000927']",
-                                  namespaces = ns, xmlAttrs)
-                  .xvals <- sapply(x, "[", "value")
-                  k <- length(.xvals)
-                  names(.xvals) <- sprintf(paste0("X%0",
-                                                  ceiling(log10(k) + 1L),
-                                                  "d.%s"),
-                                           1:k, i)
-                  ## if object only had a subset of ms levels
-                  rw <- mzR::openMSfile(fileNames(obj))
-                  hd <- mzR::header(rw)
-                  sel <- hd$msLevel %in% unique(fData(obj)$msLevel)
-                  stopifnot(k == length(sel))
-                  stopifnot(length(obj) == sum(sel))                  
-                  .xvals <- .xvals[sel]
-                  xvals[[i]] <- .xvals
-              }
-              xvals <- as.numeric(unlist(xvals))
-              stopifnot(length(xvals) == length(object))
-              fData(object)$injectionTime <- xvals
-              if (validObject(object))
-                  return(object)
-          })

R/readMSData2.R

@@ -46,11 +46,14 @@ readMSData2 <- function(files,
                         centroided = rep(as.logical(NA), nrow(fdData)),
                         smoothed = rep(as.logical(smoothed.), nrow(fdData)),
                         fdData, stringsAsFactors = FALSE)
+        injt <- injectionTimeFromFile1(f)
+        if (is.numeric(injt) && length(injt) == nrow(fdData))
+            fdData$injectionTime <- injt
         ## Order the fdData by acquisitionNum to force use of acquisitionNum
         ## as unique ID for the spectrum (issue #103). That way we can use
         ## the spIdx (is the index of the spectrum within the file) for
         ## subsetting and extracting.
-        fdData <- fdData[order(fdData$acquisitionNum), ]
+        fdData <- fdData[order(fdData$acquisitionNum), ] ## not sure this is needed
         featureDataList <- c(featureDataList, list(fdData))
         mzR::close(msdata)
         rm(msdata)