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## Copyright (C) 2020 by University of Luxembourg
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
## http://www.apache.org/licenses/LICENSE-2.0
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
## Constants
FN_FTAB_BASE<-"ftable.base.csv"
FN_FTAB_PP<-"ftable.pp.csv"
FN_PP_OUT_PREF<-"PP.filetable"
FN_FTAB_STATE<-"ftable_state.csv"
FN_FTAB_DEF_OUT<-"ftable.csv"
FN_CMP_L<-"compounds.csv"
FN_LOC_SETID <-"setid.csv"
FN_COMP_TAB<-"comprehensive.csv"
MODEMAP<-list(pH="MpHp_mass",
mH="MmHm_mass",
pNH4="MpNH4_mass",
pNa="MpNa_mass")
QANAMES <- c("MS1","MS2","Alignment","AboveNoise")
PLOT_DEF_TAGS<-NA
PLOT_DEF_SET<-NA
CEX<-0.75
RT_DIGITS=2
M_DIGITS=4
PAL="Dark2"
GUI_TAB_TITLE<-c(conf="Config",
gen="Spectra Extraction and Automatic QA",
GUI_SIDE_TITLE<-GUI_TAB_TITLE
GUI_SIDE_TITLE[["gen"]]<-"Spectra Extraction"
CHR_GRAM_X="retention time [min]"
CHR_GRAM_Y="intensity"
KEY_GLYPH='rect'
PLOT_MS1_LEG_TIT<-"peak retention time (MS1)"
PLOT_MS2_LEG_TIT<-"peak retention time (MS2)"
MS2_1ST_N<-5
EXTR_MS2_DIR<-"MS2"
EXTR_MS2_FLAG<-file.path(EXTR_MS2_DIR,'.ms2.DONE')
FTAB_CHK_NONE<-'NONE'
FTAB_CHK_AUTO<-'AUTO'
FTAB_CHK_MANL<-'MANUAL'
MS1_ERR_COARSE<-0.5 # Da
MS1_ERR_FINE<- 5 # ppm
EIC_ERR <- 0.001 # Da
RT_EXTR_ERR<-0.5 # min
RT_SHIFT_ERR <- 0.5 # min