lcmsmatching: MsDb.R comparison

comparison MsDb.R @ 2:20d69a062da3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8

author	prog
date	Thu, 02 Mar 2017 08:55:00 -0500
parents	e66bb061af06
children	fb9c0409d85c

comparison

equal deleted inserted replaced

-:253d531a0193
+:20d69a062da3
 		.mz.tol.unit <<- mztolunit
 	})
 	####################
+	# HANDLE COMPOUNDS #
+	####################
+	# Returns TRUE if this database handles compounds directly (by IDs)
+	MsDb$methods( handleCompounds = function() {
+		return(TRUE)
+	})
+	####################
 	# GET MOLECULE IDS #
 	####################
 	# Returns an integer vector of all molecule IDs stored inside the database.
-	MsDb$methods( getMoleculeIds = function() {
+	MsDb$methods( getMoleculeIds = function(max.results = NA_integer_) {
 		stop("Method getMoleculeIds() not implemented in concrete class.")
 	})
 	####################
 	# GET NB MOLECULES #
 	#################
 	# GET MZ VALUES #
 	#################
 	# Returns a numeric vector of all masses stored inside the database.
-	MsDb$methods( getMzValues = function(mode = NULL) {
+	MsDb$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
 		stop("Method getMzValues() not implemented in concrete class.")
 	})
 	#####################
 	# GET MOLECULE NAME #
 	##################
 	# GET PEAK TABLE #
 	##################
-	MsDb$methods( getPeakTable = function(molid = NA_integer_, mode = NA_character_){
+	MsDb$methods( getPeakTable = function(molid = NA_integer_, mode = NA_character_) {
 		stop("Method getPeakTable() not implemented in concrete class.")
 	})
 	##########
 	# SEARCH #
 	# col               The chromatographic column used.
 	# rt.tol            Simple retention tolerance parameter: rtinf = rt - rt.tol and rtsup = rt + rt.tol
 	# rt.tol.x          Tolerance parameter for the equations : rtinf = rt - rt.tol.x - rt ^ rt.tol.y and rtsup = rt + rt.tol.x + rt ^ rt.tol.y
 	# rt.tol.y          Tolerance parameter. See rt.tol.x parameter.
 	# attribs           Only search for peaks whose attribution is among this set of attributions.
-	# molids            Only search for peaks whose molecule ID is among this vector of integer molecule IDs. Can also be a data frame with a retention time column x.colnames$rt and a molecule ID column MSDB.TAG.molid.
+	# molids            Only search for peaks whose molecule ID is among this vector of integer molecule IDs. Can also be a data frame with a retention time column x.colnames$rt and a molecule ID column MSDB.TAG.MOLID.
 	# molids.rt.tol     Retention time tolerance used when molids parameter is a data frame (rt, id)
 	# precursor.match   Remove peaks whose molecule precursor peak has not also been matched.
 	# precursor.rt.tol
 	# Returns a data frame, listing m/z values provided in input. Several matches can be found for an m/z value, in which case several lines (the same number as the number of matches found) with the same m/z value repeated will be inserted. The m/z values will be listed in the same order as in the input. The columns of the data.frame are: mz, rt (only if present in the input), id, mztheo, col, colrt, composition, attribution.
 	MsDb$methods( searchForMzRtList = function(x = NULL, mode, shift = NULL, prec = NULL, col = NULL, rt.tol = NULL, rt.tol.x = NULL, rt.tol.y = NULL, molids = NULL, molids.rt.tol = NULL, attribs = NULL, precursor.match = FALSE, precursor.rt.tol = NULL, same.cols = FALSE, same.rows = FALSE, peak.table = FALSE) {
 			precursors.ids <- precursors.df[, cols.to.keep, drop = FALSE]
 			precursors.ids <- precursors.ids[ ! is.na(precursors.ids[[MSDB.TAG.MOLID]]), , drop = FALSE]
 			precursors.ids <- precursors.ids[ ! duplicated(precursors.ids), ]
 			# Get all matching peaks whose molecule is inside the previously obtained list of molecules
-			.self$.doSearchForMzRtList(mode = mode, shift = shift, prec = prec, col = col, rt.tol = NULL, rt.tol.x = NULL, rt.tol.y = NULL, molids = precursors.ids, molids.rt.tol = precursor.rt.tol, same.cols = same.cols, same.rows = same.rows, peak.table = peak.table)
+			df <- .self$.doSearchForMzRtList(mode = mode, shift = shift, prec = prec, col = col, rt.tol = NULL, rt.tol.x = NULL, rt.tol.y = NULL, molids = precursors.ids, molids.rt.tol = precursor.rt.tol, same.cols = same.cols, same.rows = same.rows, peak.table = peak.table)
 # TODO
 #
 #			peaks <- if (peak.table) results[['peaks']] else results
 #
 #			# Merge results with the column/rt found for precursors.
 #			z <- cbind(z, x[NULL, ! x.cols %in% colnames(z), drop = FALSE])
 #		}
 		# Loop on all lines of input
 		peaks <- NULL
+		.self$.input.stream$reset()
 		while (.self$.input.stream$hasNextValues()) {
 			.self$.input.stream$nextValues()
 				# Search for m/z
 #					y[r, colnames(x.lines)] <- x.lines
 #				}
 #				else {
 #					if (same.rows) {
 #						y[r, colnames(x.lines)] <- x.lines
-#						ids <- results[[MSDB.TAG.molid]]
+#						ids <- results[[MSDB.TAG.MOLID]]
 #						ids <- ids[ ! duplicated(ids)] # Remove duplicated values
 #						y[r, MSDB.TAG.msmatching] <- paste(ids, collapse = .self$.molids.sep)
 #					}
 #					if ( ! same.rows || peak.table) {
 #						new.rows <- cbind(x.lines, results, row.names = NULL)
 			rt.high <- if (is.null(rt.high)) high else min(high, rt.high)
 		}
 		# List molecule IDs
 		if ( ! is.null(molids.rt.tol) && is.data.frame(molids)) {
-			ids <- molids[(rt >= molids[[MSDB.TAG.colrt]] - molids.rt.tol) & (rt <= molids[[MSDB.TAG.colrt]] + molids.rt.tol), MSDB.TAG.molid]
+			ids <- molids[(rt >= molids[[MSDB.TAG.COLRT]] - molids.rt.tol) & (rt <= molids[[MSDB.TAG.COLRT]] + molids.rt.tol), MSDB.TAG.MOLID]
 			if (length(ids) == 0)
 				# No molecule ID match for this retention time
 				return(data.frame()) # return empty result set
 		} else {
 			ids <- molids

Mercurial > repos > prog > lcmsmatching

comparison MsDb.R @ 2:20d69a062da3 draft