diff MassFiledbConn.R @ 6:f86fec07f392 draft default tip

planemo upload commit c397cd8a93953798d733fd62653f7098caac30ce

--- a/MassFiledbConn.R	Wed Apr 19 10:00:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,275 +0,0 @@
-# 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.MZEXP, BIODB.PEAK.MZTHEO, 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 <- methods::setRefClass("MassFiledbConn", contains = "MassdbConn", fields = list(.file = "character", .file.sep = "character", .file.quote = "character", .field.multval.sep = 'character', .db = "ANY", .db.orig.colnames = "character", .fields = "list", .ms.modes = "character"))
-
-###############
-# CONSTRUCTOR #
-###############
-
-MassFiledbConn$methods( initialize = function(file = NA_character_, file.sep = "\t", file.quote = "\"", ...) {
-
-	# Check file
-	(! is.null(file) && ! is.na(file)) || stop("You must specify a file database to load.")
-	file.exists(file) || stop(paste0("Cannot locate the file database \"", file ,"\"."))
-
-	# Set fields
-	.db <<- NULL
-	.db.orig.colnames <<- NA_character_
-	.file <<- file
-	.file.sep <<- file.sep
-	.file.quote <<- file.quote
-	.fields <<- .BIODB.DFT.DB.FIELDS
-	.field.multval.sep <<- ';'
-	.ms.modes <<- c(BIODB.MSMODE.NEG, BIODB.MSMODE.POS)
-	names(.self$.ms.modes) <- .self$.ms.modes
-
-	callSuper(...)
-})
-
-######################
-# Is valid field tag #
-######################
-
-MassFiledbConn$methods( isValidFieldTag = function(tag) {
-	return (tag %in% names(.self$.fields))
-})
-
-###########
-# INIT DB #
-###########
-
-MassFiledbConn$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, comment.char = '')
-
-		# Save column names
-		.db.orig.colnames <<- colnames(.self$.db)
-	}
-})
-
-#############
-# Set field #
-#############
-
-MassFiledbConn$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
-	}
-
-	# Update data frame column names
-	colnames(.self$.db) <- vapply(.self$.db.orig.colnames, function(c) if (c %in% .self$.fields) names(.self$.fields)[.self$.fields %in% c] else c, FUN.VALUE = '')
-})
-
-######################################
-# SET FIELD MULTIPLE VALUE SEPARATOR #
-######################################
-
-MassFiledbConn$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$methods( getEntryContentType = function(type) {
-	return(BIODB.DATAFRAME)
-})
-
-################
-# CHECK FIELDS #
-################
-
-MassFiledbConn$methods( .check.fields = function(fields) {
-
-	if (length(fields) ==0 || (length(fields) == 1 && is.na(fields)))
-		return
-
-	# 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$.init.db()
-
-	# Check if fields are defined in file database
-	undefined.fields <- colnames(.self$.db)[ ! fields %in% colnames(.self$.db)]
-	if (length(undefined.fields) > 0)
-		stop(paste0("Column(s) ", paste(fields), collapse = ", "), " is/are undefined in file database.")
-})
-
-##########
-# SELECT #
-##########
-
-# Select data from database
-MassFiledbConn$methods( .select = function(cols = NULL, mode = NULL, compound.ids = NULL, drop = FALSE, uniq = FALSE, sort = FALSE, max.rows = NA_integer_) {
-
-	x <- NULL
-
-	# Init db
-	.self$.init.db()
-
-	# Get db
-	db <- .self$.db
-
-	# Filter db on mode
-	if ( ! is.null(mode) && ! is.na(mode)) {
-
-		# Check mode value
-		mode %in% names(.self$.ms.modes) || stop(paste0("Unknown mode value '", mode, "'."))
-		.self$.check.fields(BIODB.MSMODE)
-
-		# Filter on mode
-		db <- db[db[[unlist(.self$.fields[BIODB.MSMODE])]] %in% .self$.ms.modes[[mode]], ]
-	}
-
-	# Filter db on compound ids
-	# TODO
-
-	if ( ! is.null(cols) && ! is.na(cols))
-		.self$.check.fields(cols)
-
-	# Get subset
-	if (is.null(cols) || is.na(cols))
-		x <- db
-	else
-		x <- db[, unlist(.self$.fields[cols]), drop = drop]
-
-	# 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$methods( getEntryIds = function(type) {
-
-	ids <- NA_character_
-
-	if (type %in% c(BIODB.SPECTRUM, BIODB.COMPOUND))
-		ids <- as.character(.self$.select(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$methods( getChromCol = function(compound.ids = NULL) {
-
-	# Extract needed columns
-	db <- .self$.select(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$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
-
-	# Get mz values
-	mz <- .self$.select(cols = BIODB.PEAK.MZ, mode = mode, drop = TRUE, uniq = TRUE, sort = TRUE, max.rows = max.results)
-
-	return(mz)
-})
-
-################
-# GET NB PEAKS #
-################
-
-# Inherited from MassdbConn.
-MassFiledbConn$methods( getNbPeaks = function(mode = NULL, compound.ids = NULL) {
-
-	# Get peaks
-	peaks <- .self$.select(cols = BIODB.PEAK.MZTHEO, mode = mode, compound.ids = compound.ids)
-
-	return(length(peaks))
-})