diff MsBioDb.R @ 2:20d69a062da3 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MsBioDb.R	Thu Mar 02 08:55:00 2017 -0500
@@ -0,0 +1,100 @@
+if ( ! exists('MsBioDb')) { # Do not load again if already loaded
+
+	library(methods)
+	source('MsDb.R')
+	source(file.path('BiodbObject.R'), chdir = TRUE)
+	source(file.path('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))
+	})
+
+}