Streamline mix.R and run.R

More sensible (re)loading of the configuration files, encapsulation of
certain operations and other fixes

* mix.R(get_.*): Generate various filenames.

* mix.R(various intermediate wrappers around RMassBank calls):
  removed.

* run.R(presc.do): Adjust to changes in mix.R

* man: Update docs.

* NAMESPACE: Update exports.

man/sw.single.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{sw.single}
-\alias{sw.single}
-\title{RMassBank Spectral Workflow on a Single Compound Mixture}
-\usage{
-sw.single(fn_data, stgs_alist, wd, fn_cmpd_list, mode,
-  readMethod = "mzR", archdir = "archive", lastStep = 8)
-}
-\arguments{
-\item{fn_data}{A mzML data file.}
-
-\item{stgs_alist}{RMassBank settings. It can either be a named
-list of settings, or a filename of a YAML file.}
-
-\item{wd}{The name of the work directory.}
-
-\item{fn_cmpd_list}{The file name of he compound list
-corresponding to \code{fn_data}.}
-
-\item{mode}{Modes as described in the standard workflow vignette
-of RMassBank.}
-
-\item{readMethod}{Default read method is "mzR". Consult the
-documentation of \code{msmsRead} for details.}
-
-\item{archdir}{The directory to store R objects created during
-workflow execution.}
-
-\item{lastStep}{The last step in the workflow. Default is eight.}
-}
-\value{
-MsmsWorkspace object.
-}
-\description{
-Runs a compound mixture workflow on a single mzML file.
-}
-\author{
-Todor Kondić
-}

man/sw.single.next.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{sw.single.next}
-\alias{sw.single.next}
-\title{RMassBank Spectral Workflow on a Single Compound Mixture (after step 1)}
-\usage{
-sw.single.next(w, wd, archdir = "archive", lastStep = 8)
-}
-\arguments{
-\item{w}{The msmsWorkspace object that was processed by
-sw.single.1.}
-
-\item{wd}{The current working dir.}
-
-\item{archdir}{The directory to store R objects created during
-workflow execution.}
-
-\item{lastStep}{The last step in the workflow. Default is eight.}
-}
-\value{
-MsmsWorkspace object.
-}
-\description{
-Runs steps after sw.single.1 of compound mixture workflow on a
-single mzML file.
-}
-\author{
-Todor Kondić
-}

man/v.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{v}
-\alias{v}
-\title{Vectorised Spectral Workflow.}
-\usage{
-v(fn_data, stgs_alist, wd, fn_cmpd_list, mode, readMethod = "mzR",
-  archdir = "archive", lastStep = 8, combine = F)
-}
-\arguments{
-\item{fn_data}{A sequence of mzML input files.}
-
-\item{stgs_alist}{A list of named list of settings, or a list of
-filenames of YAML files containing the settings.}
-
-\item{wd}{The list of working directories.}
-
-\item{fn_cmpd_list}{The compound list characterising the mixtures.}
-
-\item{mode}{Same as in msmsRead.}
-
-\item{readMethod}{Same as in msmsRead.}
-
-\item{archdir}{Name of the archive.}
-
-\item{lastStep}{The last step of the spectral workflow.}
-
-\item{combine}{If TRUE, use combineMultiplicies to merge
-workspaces corresponding to different collisional energies.}
-}
-\value{
-A named list of spectral workspaces. The names are derived
-from data filenames.
-}
-\description{
-Interface to vectorised spectral workflow.
-}
-\author{
-Todor Kondić
-}