diff msdb-common.R @ 2:20d69a062da3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8

--- a/msdb-common.R	Sat Sep 03 17:02:01 2016 -0400
+++ b/msdb-common.R	Thu Mar 02 08:55:00 2017 -0500
@@ -2,38 +2,40 @@
 
 	library('stringr')
 	source('strhlp.R', chdir = TRUE)
+	source('biodb-common.R', chdir = TRUE)
 
 	#############
 	# CONSTANTS #
 	#############
 
 	# Field tags
-	MSDB.TAG.MZ <- 'mz'
-	MSDB.TAG.MZEXP <- 'mzexp'
-	MSDB.TAG.MZTHEO <- 'mztheo'
-	MSDB.TAG.RT <- 'rt'
-	MSDB.TAG.MODE <- 'mode'
-	MSDB.TAG.MOLID <- 'molid'
-	MSDB.TAG.COL <- 'col'
-	MSDB.TAG.COLRT <- 'colrt'
-	MSDB.TAG.ATTR <- 'attr'
-	MSDB.TAG.INT <- 'int' # Absolute intensity
-	MSDB.TAG.REL <- 'rel' # Relative intensity
-	MSDB.TAG.COMP <- 'comp'
-	MSDB.TAG.MOLNAMES <- 'molnames'
-	MSDB.TAG.MOLCOMP <- 'molcomp'
-	MSDB.TAG.MOLATTR <- 'molattr'
-	MSDB.TAG.MOLMASS <- 'molmass'
-	MSDB.TAG.INCHI <- 'inchi'
-	MSDB.TAG.INCHIKEY <- 'inchikey'
-	MSDB.TAG.PUBCHEM <- 'pubchem'
-	MSDB.TAG.CHEBI <- 'chebi'
-	MSDB.TAG.HMDB <- 'hmdb'
-	MSDB.TAG.KEGG <- 'kegg'
+	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
 
 	# Mode tags
-	MSDB.TAG.POS           <- 'ms.pos'
-	MSDB.TAG.NEG           <- 'ms.neg'
+	MSDB.TAG.POS           <- BIODB.MSMODE.NEG
+	MSDB.TAG.NEG           <- BIODB.MSMODE.POS
 
 	# Fields containing multiple values
 	MSDB.MULTIVAL.FIELDS <- c(MSDB.TAG.MOLNAMES)