From 51db456e7af7bf64db346668a664529cc43a1738 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Wed, 19 Jun 2019 16:59:39 +0200
Subject: [PATCH] Generate combined settings
---
R/mix.R | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/R/mix.R b/R/mix.R
index 8594f4d..168a262 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -217,19 +217,26 @@ mb.single<-function(mb,infodir,fn_stgs) {
##' from data filenames.
##' @author Todor Kondić
v<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="archive",lastStep=8,combine=F) {
+ idir<-function(n) file.path(rdir,stripext(n))
f<-Vectorize(single.sw,vectorize.args=c("wd","fn_data","stgs_alist"),SIMPLIFY=F)
rootdir <- getwd()
if (combine) {
z<-f(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod=readMethod,archdir=archdir,lastStep=7)
names(z)<-basename(fn_data)
zz<-RMassBank::combineMultiplicities(z)
+
combdir<-"combined"
archdir<-file.path(rootdir,combdir,archdir)
no_drama_mkdir(combdir)
no_drama_mkdir(archdir)
fn_arch<-file.path(archdir,"archive")
+ fn_comb_stgs <- file.path(rootdir,combdir,paste(combdir,".mzML.ini",sep=''))
+ ddirs <- sapply(names(z),idir)
+ stgs_fls <- sapply(ddirs,function(x) file.path(x,paste(x,".mzML.ini",sep='')))
+ mk_combine_file(stgs_fls,fn_comb_stgs)
+
res<-list(RMassBank::msmsWorkflow(zz, steps=8, mode=mode, archivename = fn_arch))
- names(res)<-paste(combdir,".yml",sep='') #Clearly a hack.
+ names(res)<-paste(combdir,".mzML",sep='') #Clearly a hack.
res
} else {
z<-f(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod=readMethod,archdir=archdir,lastStep=lastStep)
--
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