view LipidmapsCompound.R @ 0:e66bb061af06 draft

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

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