Removed function that makes no sense with new workspace structure

R/alternateAnalyze.R

@@ -91,8 +91,6 @@ analyzeMsMs.optimized <- function(msmsPeaks, mode="pH", detail=FALSE, run="preli
   }
 }
 
-
-#' @export
 analyzeMsMs.formula.optimized <- function(msmsPeaks, mode="pH", detail=FALSE, run="preliminary",
                                 filterSettings = getOption("RMassBank")$filterSettings,
                                 spectraList = getOption("RMassBank")$spectraList, fragData, fragDataIndex)

R/leMsmsRaw.R

@@ -848,73 +848,3 @@ addMB <- function(w, cpdID, fileName, mode){
 	w <- addPeaksManually(w, cpdID, peaklist[[1]], mode)
 	return(w)
 }
-
-
-#####
-#####Should the following function be exported or not? I guess you could, but then again, 
-#####its purpose is very specific and there is much room to misunderstand it.
-#####
-
-#' Concatenation of raw spectra in msmsWorkspace
-#' 
-#' Concatenates the (at)specs spectra of msmsWorkspace according to cpdIDs
-#'
-#' @usage c.msmsWSspecs(w1, w2)
-#' @param w1,w2 The msmsWorkspaces of which the spectra should be concatenated
-#' @return The \code{msmsWorkspace} with the spectra of two workspaces concatenated into one. Please note that the spectra from w2 will be concatenated to w1 and not vice versa.
-#' @seealso \code{\link{addPeaksManually}}
-#' @author Erik Mueller
-#' @examples \dontrun{
-#' 		c.msmsWSspecs(w1,w2)
-#' }
-#'@export
-c.msmsWSspecs <- function(w1 = NA, w2 = NA){
-
-	if(class(w1) != "msmsWorkspace" || class(w2) != "msmsWorkspace"){
-		stop("At least one of the supplied arguments is not of the msmsWorkspace class.") 
-	}
-	
-	cpdIDsw1 <- sapply(w1@specs, function(x) x$id)
-	cpdIDsw2 <- sapply(w2@specs, function(x) x$id)
-	
-	if(length(cpdIDsw2) == 0){
-		stop("w2 can't be empty.")
-	}
-	
-	if(length(cpdIDsw1) == 0){
-		w1@specs <- w2@specs
-		w1@files <- w2@files
-		return(w1)
-	}
-	
-	for(i in 1:length(cpdIDsw2)){
-		if(any(cpdIDsw2[i] == cpdIDsw1)){
-			
-			index <- which(cpdIDsw2[i] == cpdIDsw1)
-			
-				w1@specs[[index]]$peaks <- c(w1@specs[[index]]$peaks,w2@specs[[i]]$peaks)
-				w1@specs[[index]]$childScans <- c(w1@specs[[index]]$childScans,w2@specs[[i]]$childScans)
-				w1@specs[[index]]$childHeaders <- rbind(w1@specs[[index]]$childHeaders, w2@specs[[i]]$childHeaders)
-				
-				##Fake seqNums and/or acquisitionNums if the concatenation has doubled some of them
-				
-				seqNums <- w1@specs[[index]]$childHeaders[,"seqNum"]
-				if(length(seqNums) != length(unique(seqNums))){
-					w1@specs[[index]]$childHeaders[,"seqNum"] <- 2:(nrow(w1@specs[[index]]$childHeaders) + 1)
-					w1@specs[[index]]$childScans <- 2:(nrow(w1@specs[[index]]$childHeaders) + 1)
-				}
-				
-				
-				acqNums <- w1@specs[[index]]$childHeaders[,"acquisitionNum"]
-				if(length(acqNums) != length(unique(acqNums))){
-					w1@specs[[index]]$childHeaders[,"acquisitionNum"] <- 2:(nrow(w1@specs[[index]]$childHeaders) + 1)
-				}
-		}
-		
-		if(all(cpdIDsw2[i] != cpdIDsw1)){
-			w1@specs[[length(w1@specs) + 1]] <- w2@specs[[i]]
-			w1@files <- c(w1@files,w2@files[i])
-		}
-	}
-	return(w1)
-}

R/msmsRawExtensions.r

@@ -280,8 +280,6 @@ msmsRead.ticms2 <- function(w, filetable = NULL, files = NULL, cpdids = NULL,
   }
 }
 
-
-#' @export
 findMsMsHR.ticms2.d <- function(msRaw, cpdID, mode = "pH", confirmMode = 0, useRtLimit = TRUE, 
     ppmFine = getOption("RMassBank")$findMsMsRawSettings$ppmFine,
     mzCoarse = getOption("RMassBank")$findMsMsRawSettings$mzCoarse,