diff MsDbInputDataFrameStream.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/MsDbInputDataFrameStream.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,85 @@
+if ( ! exists('MsDbInputDataFrameStream')) { # Do not load again if already loaded
+
+	library(methods)
+	source('MsDbInputStream.R')
+
+	#####################
+	# CLASS DECLARATION #
+	#####################
+	
+	MsDbInputDataFrameStream <- setRefClass("MsDbInputDataFrameStream", contains = 'MsDbInputStream', fields = list( .df = "ANY", .i = "integer"))
+	
+	###############
+	# CONSTRUCTOR #
+	###############
+	
+	MsDbInputDataFrameStream$methods( initialize = function(df = data.frame(), input.fields = msdb.get.dft.input.fields(), ...) {
+
+		.df <<- df
+		.i <<- 0L
+		
+		callSuper(input.fields = input.fields, ...)
+	})
+
+	##########
+	# GET MZ #
+	##########
+
+	MsDbInputDataFrameStream$methods( getMz = function() {
+
+		if (.self$.i > 0 && .self$.i <= nrow(.self$.df) && ! is.null(.self$.input.fields[[MSDB.TAG.MZ]]))
+			return(.self$.df[.self$.i, .self$.input.fields[[MSDB.TAG.MZ]]])
+
+		return(NULL)
+	})
+
+	##########
+	# GET RT #
+	##########
+
+	MsDbInputDataFrameStream$methods( getRt = function() {
+
+		if (.self$.i > 0 && .self$.i <= nrow(.self$.df) && ! is.null(.self$.input.fields[[MSDB.TAG.RT]]))
+			return(.self$.df[.self$.i, .self$.input.fields[[MSDB.TAG.RT]]])
+
+		return(NULL)
+	})
+
+	###########
+	# GET ALL #
+	###########
+
+	MsDbInputDataFrameStream$methods( getAll = function(but = NULL) {
+
+		if (.self$.i > 0 && .self$.i <= nrow(.self$.df)) {
+
+			vals <- .self$.df[.self$.i, , drop = FALSE]
+
+			if ( ! is.null(but))
+				vals <- vals[, ! colnames(vals) %in% .self$.input.fields[but], drop = FALSE]
+
+			return(vals)
+		}
+
+		return(NULL)
+	})
+
+	###############
+	# NEXT VALUES #
+	###############
+
+	MsDbInputDataFrameStream$methods( nextValues = function() {
+
+		if (.self$.i <= nrow(.self$.df))
+			.i <<- .self$.i + 1L
+	})
+
+	###################
+	# HAS NEXT VALUES #
+	###################
+
+	MsDbInputDataFrameStream$methods( hasNextValues = function() {
+		return(.self$.i < nrow(.self$.df))
+	})
+
+} # end of load safe guard