Merge pull request #2 from MaliRemorker/devel

Devel

R/leCsvAccess.R

@@ -10,7 +10,7 @@ assign("listEnv", NULL, envir=.listEnvEnv)
 #' \code{listEnv} (which defaults to the global environment) and used by
 #' the \code{findMz}, \code{findCAS}, ... functions. The CSV file is required to have at least the following columns, which are used for 
 #' further processing and must be named correctly (but present in any order): \var{ID, Name, SMILES, RT,
-#' CAS}
+#' CAS}. If a dataframe is supplied instead of path, this can be loaded in, too.
 #' 
 #' resetList() clears a currently loaded list.
 #' 
@@ -18,10 +18,13 @@ assign("listEnv", NULL, envir=.listEnvEnv)
 #' @usage loadList(path, listEnv=NULL, check=TRUE)
 #' 
 #' resetList()
-#' @param path Path to the CSV list.
-#' @param listEnv The environment to load the list into. By default, the namelist is loaded
-#' 		into an environment internally in RMassBank. 
-#' @param check A parameter that specifies whether the SMILES-Codes in the list should be checked for readability by rcdk.
+#' @param path Path to the CSV list. Alternatively, a data.frame of a
+#'     previously read in compound list.
+#' @param listEnv The environment to load the list into. By default,
+#'     the namelist is loaded into an environment internally in
+#'     RMassBank.
+#' @param check A parameter that specifies whether the SMILES-Codes in
+#'     the list should be checked for readability by rcdk.
 #' @return No return value.
 #' @author Michael Stravs
 #' @seealso \code{\link{findMz}}
@@ -34,20 +37,29 @@ assign("listEnv", NULL, envir=.listEnvEnv)
 loadList <- function(path, listEnv = NULL, check = TRUE)
 {
 	if(is.null(listEnv))
-		listEnv <- .listEnvEnv
-	if(!file.exists(path))
-		stop("The supplied file does not exist, please supply a correct path")
-        
-    # Try out if the file is comma- or semicolon-separated
-    compoundList <- read.csv(path, stringsAsFactors=FALSE, check.names=FALSE)
-	n <- colnames(compoundList)
-    if(!("ID" %in% n)){ # If no ID column, it must be semicolon separated
-        compoundList <- read.csv2(path, stringsAsFactors=FALSE, check.names=FALSE)
+            listEnv <- .listEnvEnv
+
+        compoundList <- if (is.data.frame(path))
+                        {
+                            path
+                        } else {
+                            if(!file.exists(path))
+                                stop("The supplied file does not exist, please supply a correct path")
+                            ## Try out if the file is comma- or semicolon-separated.
+                            tmpList <- read.csv(path, stringsAsFactors=FALSE, check.names=FALSE)
+                            n <- colnames(tmpList)
+                            if(!("ID" %in% n)){ # If no ID column, it must be semicolon separated
+                                tmpList <- read.csv2(path, stringsAsFactors=FALSE, check.names=FALSE)
+                                n <- colnames(tmpList)
+                                if(!("ID" %in% n)){ # ...or there must be something wrong with the column names
+                                    stop("There is no 'ID' column in the compound list")
+                                }
+                            }
+                            tmpList
+                        }
         n <- colnames(compoundList)
-        if(!("ID" %in% n)){ # ...or there must be something wrong with the column names
-             stop("There is no 'ID' column in the compound list")
-        }
-    }
+                     
+                     
     
     # Now everything should be fine, at least regarding csv and ssv
     
@@ -626,4 +638,4 @@ findMass <- function(cpdID_or_smiles, retrieval="standard", mode = "pH")
         mol <- getMolecule(s)
         return(get.exact.mass(mol))
     }
-}
\ No newline at end of file
+}

R/msmsRead.R

@@ -495,12 +495,10 @@ msmsRead.parallel <- function(cl,w,filetable = NULL, files = NULL, cpdids = NULL
             envir <- environment()
             ## clusterExport(cl,c("count","envir")) # Have no idea what
             ##                             # for are those two.
-            doone <- function(fn) {
+
+            doone <- function(fn,cpdID) {
                 ## Find compound ID
-                cpdID <- cpdids[count]
                 retrieval <- findLevel(cpdID,TRUE)
-                ## Set counter up
-                envir$count <- envir$count + 1
 							
                 ## Retrieve spectrum data
                 spec <- findMsMsHR(fileName = fn, 
@@ -510,12 +508,13 @@ msmsRead.parallel <- function(cl,w,filetable = NULL, files = NULL, cpdids = NULL
                                    fillPrecursorScan = settings$findMsMsRawSettings$fillPrecursorScan,
                                    rtMargin = settings$rtMargin,
                                    deprofile = settings$deprofile, retrieval=retrieval)
-                message("File: ",fn,"Compound: ",cpdID,"DONE")
+                message("File: ",fn," ;Compound ID: ",cpdID,"; Status: DONE")
                 gc()
                 return(spec)
             
             }
-            cllct <- parallel::parLapply(cl,w@files,doone)
+            parallel::clusterExport(cl,c("readMethod","mode","confirmMode","useRtLimit","settings"),envir=environment())
+            cllct <- parallel::clusterMap(cl,doone,w@files,cpdids)
             w@spectra <- as(cllct,"SimpleList")
             names(w@spectra) <- basename(as.character(w@files))
             return(w)

man/dot-parseTitleString.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/createMassBank.R
+\name{.parseTitleString}
+\alias{.parseTitleString}
+\title{Parse record title}
+\usage{
+.parseTitleString(mbrecord)
+}
+\arguments{
+\item{mbrecord}{A MassBank record in list format, as returned from
+\code{\link{gatherSpectrum}}.}
+}
+\value{
+A string with the title.
+}
+\description{
+Parses a title for a single MassBank record using the title format
+specified in the option titleFormat. Internally used, not exported.
+}
+\details{
+If the option is not set, a standard title format is used (for record definition
+version 1 or 2).
+}
+\examples{
+\dontrun{
+		# used in compileRecord()
+		title <- .parseTitleString(mbrecord)
+}
+
+
+
+}
+\references{
+MassBank record format:
+\url{http://www.massbank.jp/manuals/MassBankRecord_en.pdf}
+}
+\seealso{
+\code{\link{compileRecord}}
+}
+\author{
+Michael Stravs, Eawag
+}