From 1adebc07623124f6a975dc1db62a0ce1aa71491b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Mon, 24 Jun 2019 00:14:48 +0200
Subject: [PATCH] Add presc.do

* R/run.R(presc.do): New function. Top level prescreening function.

* NAMESPACE: New exports.

* man: Update doc.
---
 NAMESPACE       |  1 +
 R/run.R         | 25 +++++++++++++++++++++++++
 man/presc.do.Rd | 27 +++++++++++++++++++++++++++
 3 files changed, 53 insertions(+)
 create mode 100644 man/presc.do.Rd

diff --git a/NAMESPACE b/NAMESPACE
index ed32db2..d1c6afe 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,7 @@
 
 export(mb.do)
 export(mb.prep)
+export(presc.do)
 export(presc.p)
 export(presc.single)
 export(presc.v)
diff --git a/R/run.R b/R/run.R
index 0479082..629a1a8 100644
--- a/R/run.R
+++ b/R/run.R
@@ -8,6 +8,31 @@
 attch<-function(...) paste(...,sep='')
 
 
+##' Do the prescreening.
+##'
+##' @title Prescreening on bunch of files.
+##' @param fn_data The mzML files. Basis for the out directory name
+##'     generation.
+##' @param fn_cmpd_list The compound list CSV.
+##' @param mode RMB mode.
+##' @param proc Amount of processors, or FALSE. 
+##' @return Nothing useful.
+##' @author Todor Kondić
+##' @export
+presc.do<-function(fn_data,fn_cmpd_list,mode,proc=F) {
+
+
+    if (proc) {
+        cl<-parallel::makeCluster(proc)
+        presc.p(fn_data,fn_cmpd_l=fn_cmpd_list,mode=mode,cl=cl)
+    } else {
+        presc.v(fn_data,fn_cmpd_l=fn_cmpd_list,mode)
+    }
+}
+
+
+
+
 ##' Performs massbank workflow on multiple mzML files:
 ##'
 ##'
diff --git a/man/presc.do.Rd b/man/presc.do.Rd
new file mode 100644
index 0000000..f001b9b
--- /dev/null
+++ b/man/presc.do.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run.R
+\name{presc.do}
+\alias{presc.do}
+\title{Prescreening on bunch of files.}
+\usage{
+presc.do(fn_data, fn_cmpd_list, mode, proc = F)
+}
+\arguments{
+\item{fn_data}{The mzML files. Basis for the out directory name
+generation.}
+
+\item{fn_cmpd_list}{The compound list CSV.}
+
+\item{mode}{RMB mode.}
+
+\item{proc}{Amount of processors, or FALSE.}
+}
+\value{
+Nothing useful.
+}
+\description{
+Do the prescreening.
+}
+\author{
+Todor Kondić
+}
-- 
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