R/io.R

In sneumann/mzR-playground: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

openMSfile <- function(filename,
                       backend=c("Ramp", "netCDF"),
                       verbose = FALSE) {
  if (!file.exists(filename))
    stop("File ",filename," not found.\n")
  filename <- path.expand(filename)
  if (missing(backend)) {
    ## Guess from file extension
    if (grepl('\\.cdf$', filename,
              ignore.case = TRUE, perl = TRUE)) {
      backend <- "netCDF"
    } else {
      ## so far everything else is handled by Ramp
      backend <- "Ramp"
    }    
  }
  
  if (tolower(backend) == "ramp") { 
    rampModule <- new( Ramp ) 
    rampModule$open(filename, declaredOnly = TRUE)
    if (!rampModule$OK()) {
      stop("Unable to create valid cRamp object.")
    }
    return(new("mzRramp",
               backend=rampModule,
               fileName=filename))
  } else if (tolower(backend) == "netcdf") { 
    if (netCDFIsFile(filename)) {
      ncid <- netCDFOpen(filename)
      if (!is.null(attr(ncid, "errortext"))) {
        stop(attr(ncid, "errortext"))
      }
##      on.exit(netCDFClose(ncid)) ## Hm, that worked in xcms ?!
      return(new("mzRnetCDF",
                 backend=ncid,
                 fileName=filename))
    } else {
      stop("Unable to open netCDF file.")
    }
  } else {
    stop("No valid backend", backend )
  }  
}