annotate MassbankConn.R @ 0:e66bb061af06 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 3529b25417f8e1a5836474c9adec4b696d35099d-dirty

if ( ! exists('MassbankConn')) { # Do not load again if already loaded

	source('BiodbConn.R')
	source('MassbankSpectrum.R')

	#####################
	# CLASS DECLARATION #
	#####################
	
	MassbankConn <- setRefClass("MassbankConn", contains = "BiodbConn")

	##########################
	# GET ENTRY CONTENT TYPE #
	##########################

	MassbankConn$methods( getEntryContentType = function(type) {
		return(if (type == RBIODB.SPECTRUM) RBIODB.TXT else NULL) 
	})

	#####################
	# GET ENTRY CONTENT #
	#####################
	
	MassbankConn$methods( getEntryContent = function(type, id) {

		if (type == RBIODB.SPECTRUM) {

			# Initialize return values
			content <- rep(NA_character_, length(id))

			# Request
			xmlstr <- .self$.scheduler$getUrl(get.entry.url(RBIODB.MASSBANK, id, RBIODB.TXT))

			# Parse XML and get text
			if ( ! is.na(xmlstr)) {
				library(XML)
				xml <-  xmlInternalTreeParse(xmlstr, asText = TRUE)
				ns <- c(ax21 = "http://api.massbank/xsd")
				returned.ids <- xpathSApply(xml, "//ax21:id", xmlValue, namespaces = ns)
				content[match(returned.ids, id)] <- xpathSApply(xml, "//ax21:info", xmlValue, namespaces = ns)
			}

			return(content)
		}

		return(NULL)
	})
	
	################
	# CREATE ENTRY #
	################
	
	# Creates a Spectrum instance from file content.
	# content       A file content, downloaded from the public database.
	# RETURN        A spectrum instance.
	MassbankConn$methods( createEntry = function(type, content, drop = TRUE) {
		return(if (type == RBIODB.SPECTRUM) createMassbankSpectrumFromTxt(content, drop = drop) else NULL)
	})
}