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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.
## Config defaults
CONF <- list(data=NA_character_,
project=getwd(),
compounds=list(known=NA_character_,
unknown=NA_character_,
sets=NA_character_))
## 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("[M+H]+"="MpHp_mass",
"[M-H]-"="MmHm_mass",
"[M+NH4]+"="MpNH4_mass",
"[M+Na]+"="MpNa_mass")
DISP_MODEMAP <- c(list("UNSET"="UNSET_MODE_ERROR"),MODEMAP)
TAG_NA <- "::UNSET::"
SET_NA <- "::UNSET::"
TAG_DEF <- TAG_NA
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"
## REST_TXT_INP<-c("fnKnownL",
## "fnUnkL",
## "fnSetId",
## "tagsInp")
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
## Comprehensive table properties
COMP_NAME_MAP <- list(RT="rt")
## COMP_NAMES <-c("ID","mz","rt","mode","set","origin","Name","SMILES")
COMP_NAME_FIRST <- c("ID","mz","rt","mode","tag","set","Name","SMILES","Files","wd")
## File table properties
FTAB_KEY=c("set","tag","mz")
FTAB_NAMES=c("ID", "mz", "rt", "tag", "mode", "set", "Name", "SMILES", "Files" , "wd","origin")
EMPTY_UNKNOWN <- dtable(ID=character(0),mz=numeric(0),RT=numeric(0),Name=character(0),CAS=character(0))
EMPTY_KNOWN <- dtable(ID=character(0),SMILES=character(0),RT=numeric(0),Name=character(0),CAS=character(0))
## Trivial data table
EMPTY_MZML <- dtable(Files=character(0),
tag=character(0),
mode=character(0),
set=character(0))