diff MassbankConn.R @ 0:e66bb061af06 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MassbankConn.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,59 @@
+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)
+	})
+}