diff LipidmapsCompound.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/LipidmapsCompound.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,70 @@
+if ( ! exists('LipidmapsCompound')) { # Do not load again if already loaded
+
+	source('BiodbEntry.R')
+	source('strhlp.R', chdir = TRUE)
+
+	#####################
+	# CLASS DECLARATION #
+	#####################
+
+	LipidmapsCompound <- setRefClass("LipidmapsCompound", contains = 'BiodbEntry')
+
+	###########
+	# FACTORY #
+	###########
+
+	createLipidmapsCompoundFromCsv <- function(contents, drop = TRUE) {
+
+		compounds <- list()
+
+		# Mapping column names
+		col2field <- list()
+		col2field[[RBIODB.NAME]] <- 'COMMON_NAME'
+		col2field[[RBIODB.ACCESSION]] <- 'LM_ID'
+		col2field[[RBIODB.KEGG.ID]] <- 'KEGG_ID'
+		col2field[[RBIODB.HMDB.ID]] <- 'HMDBID'
+		col2field[[RBIODB.MASS]] <- 'MASS'
+		col2field[[RBIODB.FORMULA]] <- 'FORMULA'
+		
+		for (text in contents) {
+
+			# Create instance
+			compound <- LipidmapsCompound$new()
+
+			# Split text in lines
+			lines <- split.str(text, sep = "\n", unlist = TRUE)
+
+			# An error occured
+			if ( ! grepl("No record found", lines[[2]])) {
+
+				# Keys on first line
+				keys <- split.str(lines[[1]], unlist = TRUE)
+
+				# Values on second line
+				values <- split.str(lines[[2]], unlist = TRUE)
+				names(values) <- keys[seq(values)]
+
+				# Get field values
+				for (field in names(col2field))
+					if (values[[col2field[[field]]]] != '-')
+						compound$setField(field, values[[col2field[[field]]]])
+
+				# Set names
+				if (values[['SYNONYMS']] != '-') {
+					# TODO
+				}
+			}
+
+			compounds <- c(compounds, compound)
+		}
+
+		# Replace elements with no accession id by NULL
+		compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x)
+
+		# If the input was a single element, then output a single object
+		if (drop && length(contents) == 1)
+			compounds <- compounds[[1]]
+	
+		return(compounds)
+	}
+}