diff MsDbOutputStream.R @ 0:e66bb061af06 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 3529b25417f8e1a5836474c9adec4b696d35099d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MsDbOutputStream.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,47 @@
+if ( ! exists('MsDbOutputStream')) { # Do not load again if already loaded
+
+	library('methods')
+	source('msdb-common.R')
+
+	#####################
+	# CLASS DECLARATION #
+	#####################
+	
+	MsDbOutputStream <- setRefClass("MsDbOutputStream", fields = list(.keep.unused = "logical", .one.line = "logical", .match.sep = "character", .output.fields = "ANY", .multval.field.sep = "character", .first.val = "logical", .ascii = "logical", .noapostrophe = "logical", .noplusminus = "logical", .nogreek = "logical"))
+	
+	###############
+	# CONSTRUCTOR #
+	###############
+	
+	#' Constructor.
+	#'
+	#' @param keep.unused   Set to \code{TRUE} if you want to keep in the output, unused columns of the input.
+	#' @param one.line      Set to \code{TRUE} if you want to output only one line for each input line.
+	#' @return
+	#' @examples
+	#' stream <- MsDbOutputDataFrameStream$new(one.line = TRUE)
+	MsDbOutputStream$methods( initialize = function(keep.unused = FALSE, one.line = FALSE, match.sep = MSDB.DFT.MATCH.SEP, output.fields = msdb.get.dft.output.fields(), multval.field.sep = MSDB.DFT.OUTPUT.MULTIVAL.FIELD.SEP, first.val = FALSE, ascii = FALSE, noapostrophe = FALSE, noplusminus = FALSE, nogreek = FALSE, ...) {
+		
+		.keep.unused <<- keep.unused
+		.one.line <<- one.line
+		.match.sep <<- match.sep
+		.output.fields <<- output.fields
+		.multval.field.sep <<- multval.field.sep
+		.first.val <<- first.val
+		.ascii <<- ascii
+		.noapostrophe <<- noapostrophe
+		.noplusminus <<- noplusminus
+		.nogreek <<- nogreek
+
+		callSuper(...)
+	})
+	
+	#################
+	# MATCHED PEAKS #
+	#################
+	
+	MsDbOutputStream$methods( matchedPeaks = function(mz, rt = NULL, unused = NULL, peaks = NULL) {
+		stop("Method matchedPeaks() not implemented in concrete class.")
+	})
+
+} # end of load safe guard