diff MassbankConn.R @ 6:f86fec07f392 draft default tip

planemo upload commit c397cd8a93953798d733fd62653f7098caac30ce

--- a/MassbankConn.R	Wed Apr 19 10:00:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-#####################
-# CLASS DECLARATION #
-#####################
-
-MassbankConn <- methods::setRefClass("MassbankConn", contains = c("RemotedbConn", "MassdbConn"), fields = list( .url = "character" ))
-
-###############
-# CONSTRUCTOR #
-###############
-
-MassbankConn$methods( initialize = function(url = NA_character_, ...) {
-
-	# Set URL
-	.url <<- if (is.null(url) || is.na(url)) BIODB.MASSBANK.EU.WS.URL else url
-
-	callSuper(...)
-})
-
-##########################
-# GET ENTRY CONTENT TYPE #
-##########################
-
-MassbankConn$methods( getEntryContentType = function() {
-	return(BIODB.TXT) 
-})
-
-#####################
-# GET ENTRY CONTENT #
-#####################
-
-MassbankConn$methods( getEntryContent = function(ids) {
-
-	# Debug
-	.self$.print.debug.msg(paste0("Get entry content(s) for ", length(ids)," id(s)..."))
-
-	URL.MAX.LENGTH <- 2083
-
-	# Initialize return values
-	content <- rep(NA_character_, length(ids))
-
-	# Loop on all
-	n <- 0
-	while (n < length(ids)) {
-
-		# Get list of accession ids to retrieve
-		accessions <- ids[(n + 1):length(ids)]
-
-		# Create URL request
-		x <- get.entry.url(class = BIODB.MASSBANK, accession = accessions, content.type = BIODB.TXT, max.length = URL.MAX.LENGTH, base.url = .self$.url)
-
-		# Debug
-		.self$.print.debug.msg(paste0("Send URL request for ", x$n," id(s)..."))
-
-		# Send request
-		xmlstr <- .self$.get.url(x$url)
-
-		# Increase number of entries retrieved
-		n <- n + x$n
-
-		# Parse XML and get text
-		if ( ! is.na(xmlstr)) {
-			xml <-  xmlInternalTreeParse(xmlstr, asText = TRUE)
-			ns <- c(ax21 = "http://api.massbank/xsd")
-			returned.ids <- xpathSApply(xml, "//ax21:id", xmlValue, namespaces = ns)
-			if (length(returned.ids) > 0)
-				content[match(returned.ids, ids)] <- xpathSApply(xml, "//ax21:info", xmlValue, namespaces = ns)
-		}
-
-		# Debug
-		.self$.print.debug.msg(paste0("Now ", length(ids) - n," id(s) left to be retrieved..."))
-	}
-
-	return(content)
-})
-
-################
-# CREATE ENTRY #
-################
-
-# Creates a Spectrum instance from file content.
-# content       A file content, downloaded from the public database.
-# RETURN        A spectrum instance.
-MassbankConn$methods( createEntry = function(content, drop = TRUE) {
-	return(createMassbankEntryFromTxt(content, drop = drop))
-})
-
-#################
-# GET MZ VALUES #
-#################
-
-MassbankConn$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
-})
-
-#################
-# GET ENTRY IDS #
-#################
-
-MassbankConn$methods( getEntryIds = function(max.results = NA_integer_) {
-
-	# Set URL
-	url <- paste0(.self$.url, 'searchPeak?mzs=1000&relativeIntensity=100&tolerance=1000&instrumentTypes=all&ionMode=Both')
-	url <- paste0(url, '&maxNumResults=', (if (is.na(max.results)) 0 else max.results))
-
-	# Send request
-	xmlstr <- .self$.get.url(url)
-
-	# Parse XML and get text
-	if ( ! is.na(xmlstr)) {
-		xml <-  xmlInternalTreeParse(xmlstr, asText = TRUE)
-		ns <- c(ax21 = "http://api.massbank/xsd")
-		returned.ids <- xpathSApply(xml, "//ax21:id", xmlValue, namespaces = ns)
-		return(returned.ids)
-	}
-})
-
-##################
-# GET NB ENTRIES #
-##################
-
-MassbankConn$methods( getNbEntries = function() {
-	return(length(.self$getEntryIds()))
-})