Mercurial > repos > prog > lcmsmatching

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

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
author prog
date Thu, 02 Mar 2017 08:55:00 -0500
parents e66bb061af06
children fb9c0409d85c
comparison
equal deleted inserted replaced
1:253d531a0193 2:20d69a062da3
1 if ( ! exists('.parse_chrom_col_desc')) { # Do not load again if already loaded 1 if ( ! exists('.parse_chrom_col_desc')) { # Do not load again if already loaded
2 2
3 library('stringr') 3 library('stringr')
4 source('strhlp.R', chdir = TRUE) 4 source('strhlp.R', chdir = TRUE)
5 source('biodb-common.R', chdir = TRUE)
5 6
6 ############# 7 #############
7 # CONSTANTS # 8 # CONSTANTS #
8 ############# 9 #############
9 10
10 # Field tags 11 # Field tags
11 MSDB.TAG.MZ <- 'mz' 12 MSDB.TAG.MZ <- BIODB.PEAK.MZ
12 MSDB.TAG.MZEXP <- 'mzexp' 13 MSDB.TAG.MZEXP <- BIODB.PEAK.MZEXP
13 MSDB.TAG.MZTHEO <- 'mztheo' 14 MSDB.TAG.MZTHEO <- BIODB.PEAK.MZTHEO
14 MSDB.TAG.RT <- 'rt' 15 MSDB.TAG.RT <- BIODB.PEAK.RT
15 MSDB.TAG.MODE <- 'mode' 16 MSDB.TAG.MODE <- BIODB.MSMODE
16 MSDB.TAG.MOLID <- 'molid' 17 MSDB.TAG.MOLID <- BIODB.COMPOUND.ID
17 MSDB.TAG.COL <- 'col' 18 MSDB.TAG.COL <- BIODB.CHROM.COL
18 MSDB.TAG.COLRT <- 'colrt' 19 MSDB.TAG.COLRT <- BIODB.CHROM.COL.RT
19 MSDB.TAG.ATTR <- 'attr' 20 MSDB.TAG.ATTR <- BIODB.PEAK.ATTR
20 MSDB.TAG.INT <- 'int' # Absolute intensity 21 MSDB.TAG.INT <- BIODB.PEAK.INTENSITY
21 MSDB.TAG.REL <- 'rel' # Relative intensity 22 MSDB.TAG.REL <- BIODB.PEAK.RELATIVE.INTENSITY
22 MSDB.TAG.COMP <- 'comp' 23 MSDB.TAG.COMP <- BIODB.PEAK.COMP
23 MSDB.TAG.MOLNAMES <- 'molnames' 24 MSDB.TAG.MOLNAMES <- BIODB.FULLNAMES
24 MSDB.TAG.MOLCOMP <- 'molcomp' 25 MSDB.TAG.MOLCOMP <- BIODB.COMPOUND.MASS
25 MSDB.TAG.MOLATTR <- 'molattr' 26 # MSDB.TAG.MOLATTR <- 'molattr'
26 MSDB.TAG.MOLMASS <- 'molmass' 27 MSDB.TAG.MOLMASS <- BIODB.COMPOUND.COMP
27 MSDB.TAG.INCHI <- 'inchi' 28 MSDB.TAG.INCHI <- BIODB.INCHI
28 MSDB.TAG.INCHIKEY <- 'inchikey' 29 MSDB.TAG.INCHIKEY <- BIODB.INCHIKEY
29 MSDB.TAG.PUBCHEM <- 'pubchem' 30 # TODO Use BIODB tags.
30 MSDB.TAG.CHEBI <- 'chebi' 31 MSDB.TAG.PUBCHEM <- BIODB.PUBCHEMCOMP.ID
31 MSDB.TAG.HMDB <- 'hmdb' 32 MSDB.TAG.CHEBI <- BIODB.CHEBI.ID
32 MSDB.TAG.KEGG <- 'kegg' 33 MSDB.TAG.HMDB <- BIODB.HMDB.ID
34 MSDB.TAG.KEGG <- BIODB.KEGG.ID
33 35
34 # Mode tags 36 # Mode tags
35 MSDB.TAG.POS <- 'ms.pos' 37 MSDB.TAG.POS <- BIODB.MSMODE.NEG
36 MSDB.TAG.NEG <- 'ms.neg' 38 MSDB.TAG.NEG <- BIODB.MSMODE.POS
37 39
38 # Fields containing multiple values 40 # Fields containing multiple values
39 MSDB.MULTIVAL.FIELDS <- c(MSDB.TAG.MOLNAMES) 41 MSDB.MULTIVAL.FIELDS <- c(MSDB.TAG.MOLNAMES)
40 MSDB.MULTIVAL.FIELD.SEP <- ';' 42 MSDB.MULTIVAL.FIELD.SEP <- ';'
41 43