diff MsBioDb.R @ 6:f86fec07f392 draft default tip

planemo upload commit c397cd8a93953798d733fd62653f7098caac30ce

--- a/MsBioDb.R	Wed Apr 19 10:00:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-if ( ! exists('MsBioDb')) { # Do not load again if already loaded
-
-	library(methods)
-	source('MsDb.R')
-	source('BiodbObject.R', chdir = TRUE)
-	source('BiodbFactory.R', chdir = TRUE)
-
-	#####################
-	# CLASS DECLARATION #
-	#####################
-	
-	MsBioDb <- setRefClass("MsBioDb", contains = "MsDb", fields = list(.massdb = "ANY"))
-	
-	###############
-	# CONSTRUCTOR #
-	###############
-	
-	MsBioDb$methods( initialize = function(massdb = NULL, ...) {
-
-		# Check bio database
-		! is.null(massdb) || stop("You must set a bio database.")
-		inherits(massdb, "MassdbConn") || stop("The bio database must inherit from MassdbConn class.")
-		.massdb <<- massdb
-
-		callSuper(...)
-	})
-
-	####################
-	# HANDLE COMPOUNDS #
-	####################
-	
-	MsBioDb$methods( handleCompounds = function() {
-		return(.self$.massdb$handlesEntryType(BIODB.COMPOUND))
-	})
-
-	####################
-	# GET MOLECULE IDS #
-	####################
-	
-	MsBioDb$methods( getMoleculeIds = function(max.results = NA_integer_) {
-		return(.self$.massdb$getEntryIds(type = BIODB.COMPOUND, max.results = max.results))
-	})
-
-	####################
-	# GET NB MOLECULES #
-	####################
-	
-	MsBioDb$methods( getNbMolecules = function() {
-		return(.self$.massdb$getNbEntries(type = BIODB.COMPOUND))
-	})
-
-	#################
-	# GET MZ VALUES #
-	#################
-
-	MsBioDb$methods( getMzValues = function(mode = NULL, max.results = NA_integer_) {
-		return(.self$.massdb$getMzValues(mode = mode, max.results = max.results))
-	})
-
-	#####################
-	# GET MOLECULE NAME #
-	#####################
-
-	MsBioDb$methods( getMoleculeName = function(molid) {
-		return(.self$.massdb$getMoleculeName(molid))
-	})
-
-	###############################
-	# GET CHROMATOGRAPHIC COLUMNS #
-	###############################
-	
-	MsBioDb$methods( getChromCol = function(molid = NULL) {
-		return(.self$.massdb$getChromCol(molid))
-	})
-
-	################
-	# FIND BY NAME #
-	################
-
-	MsBioDb$methods( findByName = function(name) {
-		return(.self$.massdb$findCompoundByName(name))
-	})
-	
-	#######################
-	# GET RETENTION TIMES #
-	#######################
-	
-	MsBioDb$methods( getRetentionTimes = function(molid, col = NA_character_) {
-		return(.self$.massdb$getRetentionTimes(molid, chrom.cols = col))
-	})
-	
-	################
-	# GET NB PEAKS #
-	################
-	
-	MsBioDb$methods( getNbPeaks = function(molid = NA_integer_, mode = NA_character_) {
-		return(.self$.massdb$getNbPeaks(compound.ids = molid, mode = mode))
-	})
-
-}