diff MassbankEntry.R @ 6:f86fec07f392 draft default tip

planemo upload commit c397cd8a93953798d733fd62653f7098caac30ce

--- a/MassbankEntry.R	Wed Apr 19 10:00:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-###########################
-# MASSBANK SPECTRUM CLASS #
-###########################
-
-MassbankEntry <- methods::setRefClass("MassbankEntry", contains = "BiodbEntry")
-
-###########
-# FACTORY #
-###########
-
-createMassbankEntryFromTxt <- function(contents, drop = TRUE) {
-
-	entries <- list()
-
-	# Define fields regex
-	regex <- character()
-	regex[[BIODB.ACCESSION]] <- "^ACCESSION: (.+)$"
-	regex[[BIODB.MSDEV]] <- "^AC\\$INSTRUMENT: (.+)$"
-	regex[[BIODB.MSDEVTYPE]] <- "^AC\\$INSTRUMENT_TYPE: (.+)$"
-	regex[[BIODB.MSTYPE]] <- "^AC\\$MASS_SPECTROMETRY: MS_TYPE (.+)$"
-	regex[[BIODB.MSPRECMZ]] <- "^MS\\$FOCUSED_ION: PRECURSOR_M/Z (.+)$"
-	regex[[BIODB.NB.PEAKS]] <- "^PK\\$NUM_PEAK: ([0-9]+)$"
-	regex[[BIODB.MSPRECANNOT]] <- "^MS\\$FOCUSED_ION: PRECURSOR_TYPE (.+)$"
-	regex[[BIODB.CHEBI.ID]] <- "^CH\\$LINK: CHEBI\\s+(.+)$"
-	regex[[BIODB.KEGG.ID]] <- "^CH\\$LINK: KEGG\\s+(.+)$"
-	regex[[BIODB.INCHI]] <- "^CH\\$IUPAC:\\s+(.+)$"
-	regex[[BIODB.INCHIKEY]] <- "^CH\\$LINK: INCHIKEY\\s+(.+)$"
-	regex[[BIODB.CHEMSPIDER.ID]] <- "^CH\\$LINK: CHEMSPIDER\\s+(.+)$"
-	regex[[BIODB.CAS.ID]] <- "^CH\\$LINK: CAS\\s+(.+)$"
-	regex[[BIODB.FORMULA]] <- "^CH\\$FORMULA:\\s+(.+)$"
-	regex[[BIODB.SMILES]] <- "^CH\\$SMILES:\\s+(.+)$"
-	regex[[BIODB.MASS]] <- "^CH\\$EXACT_MASS:\\s+(.+)$"
-	regex[[BIODB.PUBCHEMCOMP.ID]] <- "^CH\\$LINK: PUBCHEM\\s+.*CID:([0-9]+)"
-	regex[[BIODB.PUBCHEMSUB.ID]] <- "^CH\\$LINK: PUBCHEM\\s+.*SID:([0-9]+)"
-
-	for (text in contents) {
-
-		# Create instance
-		entry <- MassbankEntry$new()
-
-		if ( ! is.null(text) && ! is.na(text)) {
-
-			# Read text
-			lines <- strsplit(text, "\n")
-			for (s in lines[[1]]) {
-
-				# Test generic regex
-				parsed <- FALSE
-				for (field in names(regex)) {
-					g <- stringr::str_match(s, regex[[field]])
-					if ( ! is.na(g[1,1])) {
-						entry$setField(field, g[1,2])
-						parsed <- TRUE
-						break
-					}
-				}
-				if (parsed)
-					next
-
-				# Name
-				if (is.na(entry$getField(BIODB.NAME))) {
-					g <- stringr::str_match(s, "^CH\\$NAME:\\s+(.+)$")
-					if ( ! is.na(g[1,1]))
-						entry$setField(BIODB.NAME, g[1,2])
-				}
-		
-				# PubChem
-				g <- stringr::str_match(s, "^CH\\$LINK: PUBCHEM\\s+([0-9]+)$")
-				if ( ! is.na(g[1,1]))
-					entry$setField(BIODB.PUBCHEMSUB.ID, g[1,2])
-
-				# MS MODE
-				g <- stringr::str_match(s, "^AC\\$MASS_SPECTROMETRY: ION_MODE (.+)$")
-				if ( ! is.na(g[1,1])) {
-					entry$setField(BIODB.MSMODE, if (g[1,2] == 'POSITIVE') BIODB.MSMODE.POS else BIODB.MSMODE.NEG)
-					next
-				}
-
-				# PEAKS
-				if (.parse.peak.line(entry, s))
-					next
-			}
-		}
-
-		entries <- c(entries, entry)
-	}
-
-	# Replace elements with no accession id by NULL
-	entries <- lapply(entries, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)
-
-	# If the input was a single element, then output a single object
-	if (drop && length(contents) == 1)
-		entries <- entries[[1]]
-
-	return(entries)
-}
-
-###################
-# PARSE PEAK LINE #
-###################
-
-.parse.peak.line <- function(entry, line) {
-
-	peaks <- BIODB.PEAK.DF.EXAMPLE
-	
-	# Annotation
-	g <- stringr::str_match(line, "^\\s+([0-9][0-9.]*) ([A-Z0-9+-]+) ([0-9]+) ([0-9][0-9.]*) ([0-9][0-9.]*)$")
-	if ( ! is.na(g[1,1]))
-		peaks[1, c(BIODB.PEAK.MZ, BIODB.PEAK.FORMULA, BIODB.PEAK.FORMULA.COUNT, BIODB.PEAK.MASS, BIODB.PEAK.ERROR.PPM)] <- list(as.double(g[1,2]), g[1,3], as.integer(g[1,4]), as.double(g[1,5]), as.double(g[1,6]))
-
-	# Peak
-	g <- stringr::str_match(line, "^\\s+([0-9][0-9.]*) ([0-9][0-9.]*) ([0-9]+)$")
-	if ( ! is.na(g[1,1]))
-		peaks[1, c(BIODB.PEAK.MZ, BIODB.PEAK.INTENSITY, BIODB.PEAK.RELATIVE.INTENSITY)] <- list(as.double(g[1,2]), as.double(g[1,3]), as.integer(g[1,4]))
-
-	if (nrow(peaks) > 0) {
-
-		# Get curent peaks and merge with new peaks
-		current.peaks <- entry$getField(BIODB.PEAKS)
-		if ( ! is.null(current.peaks))
-			peaks <- rbind(current.peaks, peaks)
-
-		entry$setField(BIODB.PEAKS, peaks)
-
-		return(TRUE)
-	}
-
-	return(FALSE)
-}