diff MassbankSpectrum.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/MassbankSpectrum.R	Tue Jul 12 12:02:37 2016 -0400
@@ -0,0 +1,117 @@
+if ( ! exists('MassbankSpectrum')) { # Do not load again if already loaded
+
+	source('BiodbEntry.R')
+	source('MassbankCompound.R')
+
+	###########################
+	# MASSBANK SPECTRUM CLASS #
+	###########################
+	
+	MassbankSpectrum <- setRefClass("MassbankSpectrum", contains = "BiodbEntry")
+
+	###########
+	# FACTORY #
+	###########
+	
+	createMassbankSpectrumFromTxt <- function(contents, drop = TRUE) {
+
+		library(stringr)
+
+		spectra <- list()
+
+		# Define fields regex
+		regex <- character()
+		regex[[RBIODB.ACCESSION]] <- "^ACCESSION: (.+)$"
+		regex[[RBIODB.MSDEV]] <- "^AC\\$INSTRUMENT: (.+)$"
+		regex[[RBIODB.MSDEVTYPE]] <- "^AC\\$INSTRUMENT_TYPE: (.+)$"
+		regex[[RBIODB.MSTYPE]] <- "^AC\\$MASS_SPECTROMETRY: MS_TYPE (.+)$"
+		regex[[RBIODB.MSPRECMZ]] <- "^MS\\$FOCUSED_ION: PRECURSOR_M/Z (.+)$"
+		regex[[RBIODB.NB.PEAKS]] <- "^PK\\$NUM_PEAK: ([0-9]+)$"
+		regex[[RBIODB.MSPRECANNOT]] <- "^MS\\$FOCUSED_ION: PRECURSOR_TYPE (.+)$"
+
+		for (text in contents) {
+
+			# Create instance
+			spectrum <- MassbankSpectrum$new()
+
+			# Read text
+			lines <- strsplit(text, "\n")
+			for (s in lines[[1]]) {
+
+				# Test generic regex
+				parsed <- FALSE
+				for (field in names(regex)) {
+					g <- str_match(s, regex[[field]])
+					if ( ! is.na(g[1,1])) {
+						spectrum$setField(field, g[1,2])
+						parsed <- TRUE
+						break
+					}
+				}
+				if (parsed)
+					next
+
+				# MS MODE
+				g <- str_match(s, "^AC\\$MASS_SPECTROMETRY: ION_MODE (.+)$")
+				if ( ! is.na(g[1,1])) {
+					spectrum$setField(RBIODB.MSMODE, if (g[1,2] == 'POSITIVE') RBIODB.MSMODE.POS else RBIODB.MSMODE.NEG)
+					next
+				}
+
+				# PEAKS
+				if (.parse.peak.line(spectrum, s))
+					next
+			}
+
+			spectra <- c(spectra, spectrum)
+		}
+
+		# Replace elements with no accession id by NULL
+		spectra <- lapply(spectra, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x)
+
+		# Set associated compounds
+		compounds <- createMassbankCompoundFromTxt(contents)
+		for (i in seq(spectra))
+			if ( ! is.null(spectra[[i]]))
+				spectra[[i]]$setField(RBIODB.COMPOUND, compounds[[i]])
+
+		# If the input was a single element, then output a single object
+		if (drop && length(contents) == 1)
+			spectra <- spectra[[1]]
+
+		return(spectra)
+	}
+
+	###################
+	# PARSE PEAK LINE #
+	###################
+
+	.parse.peak.line <- function(spectrum, line) {
+
+		peaks <- RBIODB.PEAK.DF.EXAMPLE
+		
+		# Annotation
+		g <- str_match(line, "^\\s+([0-9][0-9.]*) ([A-Z0-9+-]+) ([0-9]+) ([0-9][0-9.]*) ([0-9][0-9.]*)$")
+		if ( ! is.na(g[1,1]))
+			peaks[1, c(RBIODB.PEAK.MZ, RBIODB.PEAK.FORMULA, RBIODB.PEAK.FORMULA.COUNT, RBIODB.PEAK.MASS, RBIODB.PEAK.ERROR.PPM)] <- list(as.double(g[1,2]), g[1,3], as.integer(g[1,4]), as.double(g[1,5]), as.double(g[1,6]))
+
+		# Peak
+		g <- str_match(line, "^\\s+([0-9][0-9.]*) ([0-9][0-9.]*) ([0-9]+)$")
+		if ( ! is.na(g[1,1]))
+			peaks[1, c(RBIODB.PEAK.MZ, RBIODB.PEAK.INTENSITY, RBIODB.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 <- spectrum$getField(RBIODB.PEAKS)
+			if ( ! is.null(current.peaks))
+				peaks <- rbind(current.peaks, peaks)
+
+			spectrum$setField(RBIODB.PEAKS, peaks)
+
+			return(TRUE)
+		}
+
+		return(FALSE)
+	}
+}