diff MsDbOutputDataFrameStream.R @ 6:f86fec07f392 draft default tip

planemo upload commit c397cd8a93953798d733fd62653f7098caac30ce

--- a/MsDbOutputDataFrameStream.R	Wed Apr 19 10:00:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-if ( ! exists('MsDbOutputDataFrameStream')) { # Do not load again if already loaded
-
-	library(methods)
-	source('MsDbOutputStream.R')
-	source('dfhlp.R', chdir = TRUE)
-
-	#####################
-	# CLASS DECLARATION #
-	#####################
-	
-	MsDbOutputDataFrameStream <- setRefClass("MsDbOutputDataFrameStream", contains = 'MsDbOutputStream', fields = list( .df = "ANY", .output.fields = "ANY"))
-	
-	###############
-	# CONSTRUCTOR #
-	###############
-	
-	MsDbOutputDataFrameStream$methods( initialize = function(keep.unused = FALSE, one.line = FALSE, match.sep = MSDB.DFT.MATCH.SEP, output.fields = NULL, multval.field.sep = MSDB.DFT.OUTPUT.MULTIVAL.FIELD.SEP, first.val = FALSE, ascii = FALSE, noapostrophe = FALSE, noplusminus = FALSE, nogreek = FALSE, ...) {
-		
-		callSuper(keep.unused = keep.unused, one.line = one.line, match.sep = match.sep, multval.field.sep = multval.field.sep, first.val = first.val, ascii = ascii, noapostrophe = noapostrophe, noplusminus = noplusminus, nogreek = nogreek, ...)
-
-		.df <<- data.frame()
-		.output.fields <<- output.fields
-	})
-
-	##################
-	# GET DATA FRAME #
-	##################
-	
-	MsDbOutputDataFrameStream$methods( getDataFrame = function() {
-
-		# Put at least a column name if empty
-		if (nrow(.self$.df) == 0)
-			.self$.df[[.self$.output.fields[[MSDB.TAG.MZ]]]] <- numeric()
-
-		return(.self$.df)
-	})
-	
-	# Move columns to beginning {{{1
-	
-	MsDbOutputDataFrameStream$methods( moveColumnsToBeginning = function(cols) {
-		all.cols <- colnames(.self$.df)
-		other.cols <- all.cols[ ! all.cols %in% cols]
-		cols <- cols[cols %in% all.cols]
-		.df <<- .self$.df[c(cols, other.cols)]
-	})
-
-	#################
-	# MATCHED PEAKS #
-	#################
-	
-	MsDbOutputDataFrameStream$methods( matchedPeaks = function(mz, rt = NULL, unused = NULL, peaks = NULL) {
-
-		library(plyr)
-
-		# Set input values
-		x <- data.frame(mz = mz)
-		colnames(x) <- MSDB.TAG.MZ
-		if ( ! is.null(rt)) {
-			x.rt <- data.frame(rt = rt)
-			colnames(x.rt) <- MSDB.TAG.RT
-			if (.self$.rtunit == MSDB.RTUNIT.MIN)
-				x.rt[[MSDB.TAG.RT]] <- x.rt[[MSDB.TAG.RT]] / 60
-			x <- cbind(x, x.rt)
-		}
-
-
-		# Merge input values with matched peaks
-		if ( ! is.null(peaks)) {
-
-			# No rows
-			if (nrow(peaks) == 0) {
-				# Add NA values
-				peaks[1, ] <- NA
-
-			# Process existing rows
-			} else {
-
-				# Convert RT
-				if (.self$.rtunit == MSDB.RTUNIT.MIN)
-					if (MSDB.TAG.COLRT %in% colnames(peaks))
-						peaks[[MSDB.TAG.COLRT]] <- peaks[[MSDB.TAG.COLRT]] / 60
-
-				# Process multi-value fields
-				for (c in colnames(peaks))
-					if (c %in% MSDB.MULTIVAL.FIELDS) {
-
-						# Keep only first value in multi-value fields
-						if (.self$.first.val)
-							peaks[[c]] <- vapply(peaks[[c]], function(s) split.str(s, sep = MSDB.MULTIVAL.FIELD.SEP, unlist = TRUE)[[1]], FUN.VALUE = '')
-
-						# Change separator
-						else
-							peaks[[c]] <- vapply(peaks[[c]], function(s) paste0(split.str(s, sep = MSDB.MULTIVAL.FIELD.SEP, unlist = TRUE), collapse = .self$.multval.field.sep), FUN.VALUE = '')
-
-					}
-
-				# Concatenate results in one line
-				if (.self$.one.line) {
- 					# For each column, concatenate all values in one string.
-					for (c in seq(peaks)) {
-						v <- peaks[[c]]
-						v <- v[ ! is.na(v)] # remove NA values
-						v <- v[ ! duplicated(v)] # remove duplicates
-						peaks[1, c] <- paste0(v, collapse = .self$.match.sep, FUN.VALUE = '')
-					}
-					peaks <- peaks[1, ] # Keep only first line
-				}
-			}
-
-			# Merge
-			x <- cbind(x, peaks, row.names = NULL)
-		}
-
-		# Rename columns for output
-		x <- rename.col(x, names(.self$.output.fields), .self$.output.fields)
-
-		# Add unused columns
-		if ( .self$.keep.unused && ! is.null(unused)) {
-			x <- cbind(x, unused, row.names = NULL)
-		}
-
-		# Convert strings to ASCII
-		if (.self$.ascii || .self$.noapostrophe || .self$.noplusminus || .self$.nogreek)
-			for (c in seq(x))
-				if (class(x[[c]]) == 'character') {
-					if (.self$.noapostrophe)
-						x[[c]] <- gsub("'", 'prime', x[[c]], perl = TRUE)
-					if (.self$.noplusminus)
-						x[[c]] <- gsub('±', '+-', x[[c]], perl = TRUE)
-					if (.self$.nogreek) {
-						x[[c]] <- gsub('α', 'alpha', x[[c]], perl = TRUE)
-						x[[c]] <- gsub('β', 'beta', x[[c]], perl = TRUE)
-						x[[c]] <- gsub('γ', 'gamma', x[[c]], perl = TRUE)
-						x[[c]] <- gsub('δ', 'delta', x[[c]], perl = TRUE)
-					}
-					if (.self$.ascii) {
-						x[[c]] <- gsub('[^\u0001-\u007F]', '_', x[[c]], perl = TRUE)
-					}
-				}
-
-		# Add new rows to data frame
-		.df <<- rbind.fill(.self$.df, x)
-	})
-
-} # end of load safe guard