annotate LipidmapsEntry.R @ 2:20d69a062da3 draft

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

#####################
# CLASS DECLARATION #
#####################

LipidmapsEntry <- methods::setRefClass("LipidmapsEntry", contains = 'BiodbEntry')

###########
# FACTORY #
###########

createLipidmapsEntryFromCsv <- function(contents, drop = TRUE) {

	entries <- list()

	# Mapping column names
	col2field <- list()
	col2field[[BIODB.NAME]] <- 'COMMON_NAME'
	col2field[[BIODB.ACCESSION]] <- 'LM_ID'
	col2field[[BIODB.KEGG.ID]] <- 'KEGG_ID'
	col2field[[BIODB.HMDB.ID]] <- 'HMDBID'
	col2field[[BIODB.MASS]] <- 'MASS'
	col2field[[BIODB.FORMULA]] <- 'FORMULA'
	
	for (text in contents) {

		# Create instance
		entry <- LipidmapsEntry$new()

		# Split text in lines
		lines <- split.str(text, sep = "\n", unlist = TRUE)

		# An error occured
		if ( ! grepl("No record found", lines[[2]])) {

			# Keys on first line
			keys <- split.str(lines[[1]], unlist = TRUE)

			# Values on second line
			values <- split.str(lines[[2]], unlist = TRUE)
			names(values) <- keys[seq(values)]

			# Get field values
			for (field in names(col2field))
				if (values[[col2field[[field]]]] != '-')
					entry$setField(field, values[[col2field[[field]]]])

			# Set names
			if (values[['SYNONYMS']] != '-') {
				# TODO
			}
		}

		entries <- c(entries, entry)
	}

	# Replace elements with no accession id by NULL
	entries <- lapply(entries, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)

	# If the input was a single element, then output a single object
	if (drop && length(contents) == 1)
		entries <- entries[[1]]

	return(entries)
}