diff msdb-common.R @ 6:b8f70d8216b3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty

--- a/msdb-common.R	Thu Mar 16 08:15:11 2017 -0400
+++ b/msdb-common.R	Mon Mar 27 06:27:29 2017 -0400
@@ -9,33 +9,31 @@
 	#############
 
 	# Field tags
-	MSDB.TAG.MZ <- BIODB.PEAK.MZ
-	MSDB.TAG.MZEXP <- BIODB.PEAK.MZEXP
-	MSDB.TAG.MZTHEO <- BIODB.PEAK.MZTHEO
-	MSDB.TAG.RT <- BIODB.PEAK.RT
-	MSDB.TAG.MODE <- BIODB.MSMODE
-	MSDB.TAG.MOLID <- BIODB.COMPOUND.ID
-	MSDB.TAG.COL <- BIODB.CHROM.COL
-	MSDB.TAG.COLRT <- BIODB.CHROM.COL.RT
-	MSDB.TAG.ATTR <- BIODB.PEAK.ATTR
-	MSDB.TAG.INT <- BIODB.PEAK.INTENSITY
-	MSDB.TAG.REL <- BIODB.PEAK.RELATIVE.INTENSITY
-	MSDB.TAG.COMP <- BIODB.PEAK.COMP
-	MSDB.TAG.MOLNAMES <- BIODB.FULLNAMES
-	MSDB.TAG.MOLCOMP <- BIODB.COMPOUND.MASS
-#	MSDB.TAG.MOLATTR <- 'molattr'
-	MSDB.TAG.MOLMASS <- BIODB.COMPOUND.COMP
-	MSDB.TAG.INCHI <- BIODB.INCHI
-	MSDB.TAG.INCHIKEY <- BIODB.INCHIKEY
-	# TODO Use BIODB tags.
-	MSDB.TAG.PUBCHEM <- BIODB.PUBCHEMCOMP.ID
-	MSDB.TAG.CHEBI <- BIODB.CHEBI.ID
-	MSDB.TAG.HMDB <- BIODB.HMDB.ID
-	MSDB.TAG.KEGG <- BIODB.KEGG.ID
+	MSDB.TAG.MZ <- 'mz'
+	MSDB.TAG.MZEXP <- 'mzexp'
+	MSDB.TAG.MZTHEO <- 'mztheo'
+	MSDB.TAG.RT <- 'rt'
+	MSDB.TAG.MODE <- 'msmode'
+	MSDB.TAG.MOLID <- 'compoundid'
+	MSDB.TAG.COL <- 'chromcol'
+	MSDB.TAG.COLRT <- 'chromcolrt'
+	MSDB.TAG.ATTR <- 'peakattr'
+	MSDB.TAG.INT <- 'intensity'
+	MSDB.TAG.REL <- 'relative.intensity'
+	MSDB.TAG.COMP <- 'peakcomp'
+	MSDB.TAG.MOLNAMES <- 'fullnames'
+	MSDB.TAG.MOLCOMP <- 'compoundmass'
+	MSDB.TAG.MOLMASS <- 'compoundcomp'
+	MSDB.TAG.INCHI <- 'inchi'
+	MSDB.TAG.INCHIKEY <- 'inchikey'
+	MSDB.TAG.PUBCHEM <- 'pubchemcompid'
+	MSDB.TAG.CHEBI <- 'chebiid'
+	MSDB.TAG.HMDB <- 'hmdbid'
+	MSDB.TAG.KEGG <- 'keggid'
 
 	# Mode tags
-	MSDB.TAG.POS           <- BIODB.MSMODE.NEG
-	MSDB.TAG.NEG           <- BIODB.MSMODE.POS
+	MSDB.TAG.POS           <- 'neg'
+	MSDB.TAG.NEG           <- 'pos'
 
 	# Fields containing multiple values
 	MSDB.MULTIVAL.FIELDS <- c(MSDB.TAG.MOLNAMES)
@@ -47,7 +45,7 @@
 	MSDB.MZTOLUNIT.VALS <- c(MSDB.MZTOLUNIT.PPM, MSDB.MZTOLUNIT.PLAIN)
 
 	# Authorized rt units
-	MSDB.RTUNIT.SEC <- 's'
+	MSDB.RTUNIT.SEC <- 'sec'
 	MSDB.RTUNIT.MIN <- 'min'
 	MSDB.RTUNIT.VALS <- c(MSDB.RTUNIT.SEC ,MSDB.RTUNIT.MIN)
 
@@ -55,7 +53,6 @@
 	MSDB.DFT.PREC <- list()
 	MSDB.DFT.PREC[[MSDB.TAG.POS]] <- c("[(M+H)]+", "[M+H]+", "[(M+Na)]+", "[M+Na]+", "[(M+K)]+", "[M+K]+")
 	MSDB.DFT.PREC[[MSDB.TAG.NEG]] <- c("[(M-H)]-", "[M-H]-", "[(M+Cl)]-", "[M+Cl]-")
-	MSDB.DFT.OUTPUT.FIELDS <- list( mz = 'mz', rt = 'rt', col = 'col', colrt = 'colrt', molid = 'id', attr = 'attribution', comp = 'composition', int = 'intensity', rel = 'relative', mzexp = 'mzexp', mztheo = 'mztheo', msmatching = 'msmatching', molnames = 'molnames', molcomp = 'molcomp', molmass = 'molmass', inchi = 'inchi', inchikey = 'inchikey', pubchem = 'pubchem', chebi = 'chebi', hmdb = 'hmdb', kegg = 'kegg')
 	MSDB.DFT.OUTPUT.MULTIVAL.FIELD.SEP <- MSDB.MULTIVAL.FIELD.SEP
 	MSDB.DFT.MATCH.FIELDS <- list( molids = 'molid', molnames = 'molnames')
 	MSDB.DFT.MATCH.SEP <- ','
@@ -76,20 +73,6 @@
 		return(dft.fields)
 	}
 
-	#############################
-	# GET DEFAULT OUTPUT FIELDS #
-	#############################
-
-	msdb.get.dft.output.fields <- function () {
-
-		dft.fields <- list()
-
-		for(f in c(MSDB.TAG.MZ, MSDB.TAG.RT, MSDB.TAG.COL, MSDB.TAG.COLRT, MSDB.TAG.MOLID, MSDB.TAG.ATTR, MSDB.TAG.COMP, MSDB.TAG.INT, MSDB.TAG.REL, MSDB.TAG.MZEXP, MSDB.TAG.MZTHEO, MSDB.TAG.MOLNAMES, MSDB.TAG.MOLCOMP, MSDB.TAG.MOLMASS, MSDB.TAG.INCHI, MSDB.TAG.INCHIKEY, MSDB.TAG.PUBCHEM, MSDB.TAG.CHEBI, MSDB.TAG.HMDB, MSDB.TAG.KEGG))
-			dft.fields[[f]] <- f
-
-		return(dft.fields)
-	}
-
 	#########################
 	# GET DEFAULT DB FIELDS #
 	#########################
@@ -123,7 +106,7 @@
 	# MAKE INPUT DATA FRAME #
 	#########################
 
-	msdb.make.input.df <- function(mz, rt = NULL) {
+	msdb.make.input.df <- function(mz, rt = NULL, rtunit = MSDB.RTUNIT.SEC) {
 
 		field <- msdb.get.dft.input.fields()
 
@@ -139,6 +122,8 @@
 
 		# Set rt
 		if ( ! is.null(rt)) {
+			if (rtunit == MSDB.RTUNIT.MIN)
+				rtunit <- rtunit * 60
 			if (length(rt) > 1)
 				x[seq(rt), field[[MSDB.TAG.RT]]] <- rt
 			else if (length(rt) == 1)