diff MassFiledbConn.R @ 1:253d531a0193 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MassFiledbConn.R	Sat Sep 03 17:02:01 2016 -0400
@@ -0,0 +1,258 @@
+if ( ! exists('MassFiledbConn')) {
+
+	source('MassdbConn.R')
+	
+	# LCMS File db.
+	# In this type of database, a single file is provided in CSV format. Default separator is tabulation.
+	# Each line is a MS peak measure, .
+	# The file contains molecule and spectrum information. Each spectrum has an accession id.
+
+	# TODO Rename setField into setFieldName + addNewField, and setMsMode into setMsModeValue
+
+	#############
+	# CONSTANTS #
+	#############
+
+	# Default database fields
+	.BIODB.DFT.DB.FIELDS <- list()
+	for (f in c(BIODB.ACCESSION, BIODB.NAME, BIODB.FULLNAMES, BIODB.COMPOUND.ID, BIODB.MSMODE, BIODB.PEAK.MZ, BIODB.PEAK.COMP, BIODB.PEAK.ATTR, BIODB.CHROM.COL, BIODB.CHROM.COL.RT, BIODB.FORMULA, BIODB.MASS))
+		.BIODB.DFT.DB.FIELDS[[f]] <- f
+
+	#####################
+	# CLASS DECLARATION #
+	#####################
+	
+	MassFiledbConn <- setRefClass("MassFiledbConn", contains = "MassdbConn", fields = list(.file = "character", .file.sep = "character", .file.quote = "character", .field.multval.sep = 'character', .db = "ANY", .fields = "list", .ms.modes = "character"))
+
+	###############
+	# CONSTRUCTOR #
+	###############
+
+	MassFiledbConn$methods( initialize = function(file = NA_character_, file.sep = "\t", file.quote = "\"", ...) {
+
+		# Check file
+		(! is.null(file) && ! is.na(file)) || stop("You must specify a file database to load.")
+		file.exists(file) || stop(paste0("Cannot locate the file database \"", file ,"\"."))
+
+		# Set fields
+		.db <<- NULL
+		.file <<- file
+		.file.sep <<- file.sep
+		.file.quote <<- file.quote
+		.fields <<- .BIODB.DFT.DB.FIELDS
+		.field.multval.sep <<- ';'
+		.ms.modes <<- c(BIODB.MSMODE.NEG, BIODB.MSMODE.POS)
+		names(.self$.ms.modes) <- .self$.ms.modes
+
+		callSuper(...)
+	})
+
+	######################
+	# Is valid field tag #
+	######################
+
+	MassFiledbConn$methods( isValidFieldTag = function(tag) {
+		return (tag %in% names(.self$.fields))
+	})
+
+	#############
+	# Set field #
+	#############
+
+	MassFiledbConn$methods( setField = function(tag, colname) {
+
+		( ! is.null(tag) && ! is.na(tag)) || stop("No tag specified.")
+		( ! is.null(colname) && ! is.na(colname)) || stop("No column name specified.")
+
+		# Load database file
+		.self$.init.db()
+
+		# Check that this field tag is defined in the fields list
+		.self$isValidFieldTag(tag) || stop(paste0("Database field tag \"", tag, "\" is not valid."))
+
+		# Check that columns are defined in database file
+		all(colname %in% names(.self$.db)) || stop(paste0("One or more columns among ", paste(colname, collapse = ", "), " are not defined in database file."))
+
+		# Set new definition
+		if (length(colname) == 1)
+			.fields[[tag]] <<- colname
+		else {
+			new.col <- paste(colname, collapse = ".")
+			.self$.db[[new.col]] <- vapply(seq(nrow(.self$.db)), function(i) { paste(.self$.db[i, colname], collapse = '.') }, FUN.VALUE = '')
+			.fields[[tag]] <<- new.col
+		}
+	})
+
+	######################################
+	# SET FIELD MULTIPLE VALUE SEPARATOR #
+	######################################
+
+	MassFiledbConn$methods( setFieldMultValSep = function(sep) {
+		.field.multval.sep <<- sep
+	})
+
+	################
+	# SET MS MODES #
+	################
+
+	MassFiledbConn$methods( setMsMode = function(mode, value) {
+		.self$.ms.modes[[mode]] <- value
+	})
+
+	##########################
+	# GET ENTRY CONTENT TYPE #
+	##########################
+
+	MassFiledbConn$methods( getEntryContentType = function(type) {
+		return(BIODB.DATAFRAME)
+	})
+
+	###########
+	# INIT DB #
+	###########
+
+	MassFiledbConn$methods( .init.db = function() {
+
+		if (is.null(.self$.db)) {
+
+			# Load database
+			.db <<- read.table(.self$.file, sep = .self$.file.sep, .self$.file.quote, header = TRUE, stringsAsFactors = FALSE, row.names = NULL)
+
+			# Rename columns
+			colnames(.self$.db) <- vapply(colnames(.self$.db), function(c) if (c %in% .self$.fields) names(.self$.fields)[.self$.fields %in% c] else c, FUN.VALUE = '')
+		}
+	})
+
+	################
+	# CHECK FIELDS #
+	################
+
+	MassFiledbConn$methods( .check.fields = function(fields) {
+
+		# Check if fields are known
+		unknown.fields <- names(.self$.fields)[ ! fields %in% names(.self$.fields)]
+		if (length(unknown.fields) > 0)
+			stop(paste0("Field(s) ", paste(fields, collapse = ", "), " is/are unknown."))
+
+		# Init db
+		.self$.init.db()
+
+		# Check if fields are defined in file database
+		undefined.fields <- colnames(.self$.init.db)[ ! unlist(.self$.fields[fields]) %in% colnames(.self$.init.db)]
+		if (length(undefined.fields) > 0)
+			stop(paste0("Column(s) ", paste(unlist(.self$.fields[fields]), collapse = ", "), " is/are undefined in file database."))
+	})
+
+	################
+	# EXTRACT COLS #
+	################
+	
+	MassFiledbConn$methods( .extract.cols = function(cols, mode = NULL, drop = FALSE, uniq = FALSE, sort = FALSE, max.rows = NA_integer_) {
+	
+		x <- NULL
+
+		if ( ! is.null(cols) && ! is.na(cols)) {
+
+			# Init db
+			.self$.init.db()
+
+			# TODO check existence of cols/fields
+
+			# Get db, eventually filtering it.
+			if (is.null(mode))
+				db <- .self$.db
+			else {
+				# Check mode value
+				mode %in% names(.self$.ms.modes) || stop(paste0("Unknown mode value '", mode, "'."))
+				.self$.check.fields(BIODB.MSMODE)
+
+				# Filter on mode
+				db <- .self$.db[.self$.db[[unlist(.self$.fields[BIODB.MSMODE])]] %in% .self$.ms.modes[[mode]], ]
+			}
+
+			# Get subset
+			x <- db[, unlist(.self$.fields[cols]), drop = drop]
+
+			# Rename columns
+			if (is.data.frame(x))
+				colnames(x) <- cols
+
+			# Rearrange
+			if (drop && is.vector(x)) {
+				if (uniq)
+					x <- x[ ! duplicated(x)]
+				if (sort)
+					x <- sort(x)
+			}
+
+			# Cut
+			if ( ! is.na(max.rows))
+				x <- if (is.vector(x)) x[1:max.rows] else x[1:max.rows, ]
+		}
+
+		return(x)
+	})
+
+	#################
+	# GET ENTRY IDS #
+	#################
+	
+	MassFiledbConn$methods( getEntryIds = function(type) {
+
+		ids <- NA_character_
+
+		if (type %in% c(BIODB.SPECTRUM, BIODB.COMPOUND))
+			ids <- as.character(.self$.extract.cols(if (type == BIODB.SPECTRUM) BIODB.ACCESSION else BIODB.COMPOUND.ID, drop = TRUE, uniq = TRUE, sort = TRUE))
+
+		return(ids)
+	})
+
+	##################
+	# GET NB ENTRIES #
+	##################
+	
+	MassFiledbConn$methods( getNbEntries = function(type) {
+		return(length(.self$getEntryIds(type)))
+	})
+
+	###############################
+	# GET CHROMATOGRAPHIC COLUMNS #
+	###############################
+	
+	# Inherited from MassdbConn.
+	MassFiledbConn$methods( getChromCol = function(compound.ids = NULL) {
+
+		# Extract needed columns
+		db <- .self$.extract.cols(c(BIODB.COMPOUND.ID, BIODB.CHROM.COL))
+
+		# Filter on molecule IDs
+		if ( ! is.null(compound.ids))
+			db <- db[db[[BIODB.COMPOUND.ID]] %in% compound.ids, ]
+
+		# Get column names
+		cols <- db[[BIODB.CHROM.COL]]
+
+		# Remove duplicates
+		cols <- cols[ ! duplicated(cols)]
+
+		# Make data frame
+		chrom.cols <- data.frame(cols, cols, stringsAsFactors = FALSE)
+		colnames(chrom.cols) <- c(BIODB.ID, BIODB.TITLE)
+
+		return(chrom.cols)
+	})
+	
+	#################
+	# GET MZ VALUES #
+	#################
+	
+	# Inherited from MassdbConn.
+	MassFiledbConn$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
+
+		# Get mz values
+		mz <- .self$.extract.cols(BIODB.PEAK.MZ, mode = mode, drop = TRUE, uniq = TRUE, sort = TRUE, max.rows = max.results)
+
+		return(mz)
+	})
+
+}