R/importMzMl-functions.R

In sgibb/MALDIquantForeign: Import/Export Routines for 'MALDIquant'

## Copyright 2012 Sebastian Gibb
## <mail@sebastiangibb.de>
##
## This file is part of MALDIquantForeign for R and related languages.
##
## MALDIquantForeign is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## MALDIquantForeign is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with MALDIquantForeign. If not, see <https://www.gnu.org/licenses/>

.importMzMl <- function(file, centroided=FALSE, massRange=c(0, Inf),
                        minIntensity=0, verbose=FALSE) {

  .msg(verbose, "Reading spectrum from ", sQuote(file), " ...")

  if (!file.exists(file)) {
    stop("File ", sQuote(file), " doesn't exists!")
  }

  s <- .parseMzMl(file=file, verbose=verbose)

  lapply(s$spectra, function(x, globalS=s) {
    m <- modifyList(s$metaData, x$metaData)
    m$file <- file
    .createMassObject(mass=x$mass, intensity=x$intensity, snr=x$snr,
                      metaData=m, centroided=centroided,
                      massRange=massRange, minIntensity=minIntensity,
                      verbose=verbose)
  })
}