Add many things

DESCRIPTION

@@ -21,4 +21,5 @@ Collate:
     'run.R'
 Imports: 
     RMassBank,
-    parallel
+    parallel,
+    yaml

R/mix.R

@@ -26,19 +26,38 @@ no_drama_mkdir<-function(path) {
 ##' @param file The name of the YAML specification that will be merged
 ##'     with the template Rmb settings file.
 ##' @return NULL
-##' @author Todor Kondić
 mk_sett_file<-function(sett_alist,file) {
-    require(yaml)
     tmp<-tempfile()
     RMassBank::RmbSettingsTemplate(tmp)
-    sett<-yaml.load_file(tmp)
+    sett<-yaml::yaml.load_file(tmp)
     for (nm in names(sett_alist)) {
         sett[[nm]]<-sett_alist[[nm]]
     }
-    write_yaml(x=sett,file=file)
+    yaml::write_yaml(x=sett,file=file)
     NULL
 }
 
+##' Combine RMB settings with different collisional energies into one
+##' settings file with multiple collisional energy entries.
+##'
+##' .. content for \details{} ..
+##' @title Combine RMB Settings With Different Collisional Energies
+##' @param sett_fns A list of settings files.
+##' @param fname The name of the combined file.
+##' @return fname
+##' @author Todor Kondić
+mk_combine_file<-function(sett_fns,fname) {
+    all_settings <- lapply(sett_fns,yaml::yaml.load_file)
+    comb_settings <- all_settings[[1]]
+    
+    for (n in 1:length(all_settings)) {
+        comb_settings$spectraList[[n]] <- all_settings[[n]]$spectraList[[1]]
+    }
+
+    yaml::write_yaml(x=comb_settings,fname)
+    fname
+}
+
 ##' Generate the RMassBank compound list from the input compound list
 ##' in CSV file src_fn. The input compound list format is either a
 ##' Chemical Dashboard csv file with, at least, PREFERRED_ SMILES
@@ -90,11 +109,8 @@ gen_comp_list<-function(src_fn,dest_fn) {
 ##' @return MsmsWorkspace object.
 ##' @author Todor Kondić
 single.sw<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="archive",lastStep=8) {
-    
-    require(RMassBank)
-    require(yaml)
     ## Generate settings file and load.
-    stgs_alist<-if (is.character(stgs_alist)) yaml.load_file(stgs_alist) else stgs_alist
+    stgs_alist<-if (is.character(stgs_alist)) yaml::yaml.load_file(stgs_alist) else stgs_alist
     sfn<-file.path(wd,paste(fn_data,".ini",sep=''))
     mk_sett_file(stgs_alist,sfn)
     RMassBank::loadRmbSettings(sfn)

man/mb.do.Rd

@@ -4,12 +4,15 @@
 \alias{mb.do}
 \title{Perform the Mass Bank workflow}
 \usage{
-mb.do(mb, rdir = ".")
+mb.do(mb, rdir = ".", proc = F)
 }
 \arguments{
 \item{mb}{The list of prepared mbWorkspace objects.}
 
 \item{rdir}{Root data dir.}
+
+\item{proc}{Split work between this amount of processes. If FALSE
+(or, 1), run sequential.}
 }
 \value{
 The named list of processed mbWorkspace objects.

man/mb.p.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mix.R
+\name{mb.p}
+\alias{mb.p}
+\title{Parallel Mass Bank Workflow}
+\usage{
+mb.p(mb, infodir, fn_stgs, cl = F)
+}
+\arguments{
+\item{mb}{List of mass bank workflow objects}
+
+\item{infodir}{List of subdirs containing info lists.}
+
+\item{fn_stgs}{List of settings files.}
+
+\item{cl}{Cluster.}
+}
+\value{
+A named list of mbWorkspace objects. The names are derived
+from the input mb sequence.
+}
+\description{
+Interface to parallelised Mass Bank workflow.
+}
+\author{
+Todor Kondić
+}

man/mb.prep.Rd

@@ -10,6 +10,8 @@ mb.prep(w, rdir = ".")
 \item{w}{A list of spectral workspace inputs.}
 
 \item{rdir}{Data root.}
+
+\item{proc}{Split work between this amount of processes. If FALSE}
 }
 \value{
 Named list of prepared mbWorkspace objects.

man/mk_combine_file.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mix.R
+\name{mk_combine_file}
+\alias{mk_combine_file}
+\title{Combine RMB Settings With Different Collisional Energies}
+\usage{
+mk_combine_file(sett_fns, fname)
+}
+\arguments{
+\item{sett_fns}{A list of settings files.}
+
+\item{fname}{The name of the combined file.}
+}
+\value{
+fname
+}
+\description{
+Combine RMB settings with different collisional energies into one
+settings file with multiple collisional energy entries.
+}
+\details{
+.. content for \details{} ..
+}
+\author{
+Todor Kondić
+}

man/mk_sett_file.Rd

@@ -20,6 +20,3 @@ Produce the Rmb Settings file
 Produce the Rmb Settings file based on the customisation file in
 YAML format.
 }
-\author{
-Todor Kondić
-}