Works now, even if some spectra aren't found

R/leMsMs.r

@@ -117,30 +117,8 @@ msmsWorkflow <- function(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRec
 		
 		for(i in 1:length(unique(cpdIDs))){
 			specs <- list()
-			specsNull <- list()
-			specsNotNull <- list()
 			for(j in 1:length(files[[i]])){
 				specs[[j]] <- findMsMsHRperxcms.direct(files[[i]][j], unique(cpdIDs)[i], mode=mode, findPeaksArgs=findPeaksArgs, plots)	
-				specsNull[[j]] <- vector()
-				specsNotNull[[j]] <- vector()
-				for(k in 1:length(specs[[j]]))
-					if(is.null(specs[[j]][[k]])){
-						specsNull[[j]] <- c(specsNull[[j]],k)
-					} else {specsNotNull <- c(specsNotNull[[j]],k)}
-			}
-			
-			if(length(specsNotNull) == 0){
-				stop("Couldn't find any peaks that fit criteria")
-			}
-			
-			##This replaces the specs that are missing with specs already present
-			##Couldn't think of a better solution
-			for(j in length(specsNull)){
-				warning("A spectrum has been replaced because XCMS couldn't find any fitting peaks")
-				for(k in specsNull[[j]]){
-					print(specsNotNull[[j]][1])
-					specs[[j]][[k]] <- specs[[j]][[specsNotNull[[j]][1]]]
-				}
 			}
 			w@specs[[i]] <- toRMB(unlist(specs, recursive = FALSE), unique(cpdIDs)[i], mode=mode)
 		}
@@ -306,7 +284,7 @@ msmsWorkflow <- function(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRec
 #' \item{list("id")}{ 
 #' 		The compound ID (inherited from \code{msmsdata})}
 #' \item{list("mode")}{
-#' 		processing mode} $
+#' 		processing mode} 
 #' \item{list("parentHeader")}{ 
 #' 		Parent spectrum header data (ex \code{msmsdata})} 
 #' \item{list("parentMs")}{ 

R/leMsmsRaw.R

@@ -253,8 +253,8 @@ findMsMsHRperxcms.direct <- function(fileName, cpdID, mode="pH", findPeaksArgs,
 	
 	xrs <- split(msn2xcmsRaw(xrmsms), f=xrmsms@msnCollisionEnergy)
 	## Fake s simplistic xcmsSet
-	xsmsms <- as.list(replicate(length(xrs),xcmsSet(files=fileName,
-					method="MS1")))
+	setReplicate <- xcmsSet(files=fileName, method="MS1")
+	xsmsms <- as.list(replicate(length(xrs),setReplicate))
 	candidates <- list()
 	anmsms <- list()
 	psp <- list()
@@ -350,6 +350,17 @@ findEIC <- function(msRaw, mz, limit = NULL, rtLimit = NA)
 #' }
 #' @export
 toRMB <- function(msmsXCMSspecs = NA, cpdID = NA, mode="pH", MS1spec = NA){
+	
+	ret <- list()
+	ret$mz <- findMz(cpdID,mode=mode)
+	ret$id <- cpdID
+	ret$formula <- findFormula(cpdID)
+	print(paste("Length of msmsXCMSspecs:",length(msmsXCMSspecs)))
+	if(length(msmsXCMSspecs) == 0){
+		ret$foundOK <- FALSE
+		print("blabla")
+		return(ret)
+	}
 	if(is.na(msmsXCMSspecs)){
 			stop("You need a readable spectrum!")
 	}
@@ -357,11 +368,12 @@ toRMB <- function(msmsXCMSspecs = NA, cpdID = NA, mode="pH", MS1spec = NA){
 			stop("Please supply the compoundID!")
 	}
 	numScan <- length(msmsXCMSspecs)
-	ret <- list()
-	ret$foundOK <- 1
+
+	
+	ret$foundOK <- TRUE
 	ret$parentscan <- 1
 	ret$parentHeader <- matrix(0, ncol = 20, nrow = 1)
-	rownames(ret$parentHeader) <-1
+	rownames(ret$parentHeader) <- 1
 	colnames(ret$parentHeader) <- c("seqNum", "acquisitionNum", "msLevel", "peaksCount", "totIonCurrent", "retentionTime", "basepeakMZ", 
 									"basePeakIntensity", "collisionEnergy", "ionisationEnergy", "lowMZ", "highMZ", "precursorScanNum",
 									"precursorMZ", "precursorCharge", "precursorIntensity", "mergedScan", "mergedResultScanNum", 
@@ -427,9 +439,6 @@ toRMB <- function(msmsXCMSspecs = NA, cpdID = NA, mode="pH", MS1spec = NA){
 									peaks[,2] <- specs[,7]
 									return(peaks)
 								})
-	ret$mz <- findMz(cpdID,mode=mode)
-	ret$id <- cpdID
-	ret$formula <- findFormula(cpdID)
 	return(ret)
 }