annotate EnzymeEntry.R @ 2:20d69a062da3 draft

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

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

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

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

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

	entries <- list()

	# Define fields regex
	regex <- character()
	regex[[BIODB.ACCESSION]] <- "^ID\\s+([0-9.]+)$"
	regex[[BIODB.DESCRIPTION]] <- "^DE\\s+(.+)$"

	for (text in contents) {

		# Create instance
		entry <- EnzymeEntry$new()

		lines <- strsplit(text, "\n")
		for (s in lines[[1]]) {

			# Test generic regex
			parsed <- FALSE
			for (field in names(regex)) {
				g <- stringr::str_match(s, regex[[field]])
				if ( ! is.na(g[1,1])) {
					entry$setField(field, g[1,2])
					parsed <- TRUE
					break
				}
			}
			if (parsed)
				next
		}

		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)
}