Changed method name from simple to minimal

R/leMsMs.r

@@ -88,7 +88,7 @@ msmsWorkflow <- function(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRec
   nProg <- 0
   nLen <- length(w@files)
   
-  if(readMethod == "simple"){
+  if(readMethod == "minimal"){
 	##Edit options
 	opt <- getOption("RMassBank")
 	opt$recalibrator$MS1 <- "recalibrate.identity"
@@ -161,7 +161,7 @@ msmsWorkflow <- function(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRec
 	##	names(w@specs) <- basename(as.character(w@files))
 	##}
 		
-	if((readMethod == "peaklist") || (readMethod == "simple")){
+	if((readMethod == "peaklist") || (readMethod == "minimal")){
 		splitfn <- strsplit(basename(w@files), "_")
 		cpdIDs <- sapply(splitfn, function(splitted) {
 			as.numeric(return(splitted[2]))

R/msmsRead.R

@@ -75,7 +75,7 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
 	if(length(w@files) != length(cpdids)){
 		stop("There are a different number of cpdids than files")
 	}
-	if(!(readMethod %in% c("mzR","peaklist","xcms","simple"))){
+	if(!(readMethod %in% c("mzR","peaklist","xcms","minimal"))){
 		stop("The supplied method does not exist")
 	}
 	if(!all(file.exists(w@files))){
@@ -83,7 +83,7 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
 	}
 
 	##This should work
-	if(readMethod == "simple"){
+	if(readMethod == "minimal"){
 		##Edit options
 		opt <- getOption("RMassBank")
 		opt$recalibrator$MS1 <- "recalibrate.identity"
@@ -121,7 +121,7 @@ msmsRead <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
 	}
 	
 	##Peaklist-readmethod 
-	if((readMethod == "peaklist") || (readMethod=="simple")){
+	if((readMethod == "peaklist") || (readMethod=="minimal")){
 		w <- createSpecsFromPeaklists(w, cpdids, filenames=w@files, mode=mode)
 		uIDs <- unique(cpdids)
 		files <- list()