Example of an on-disk MassSpectrum class for MALDIquant

MassSpectrumOnDisk.R

library("MALDIquant")

setClass("MassSpectrumOnDisk",
         slots=list(path="character", n="numeric"),
         prototype=list(mass=numeric(), intensity=numeric(), metaData=list(),
                        path=character(), n=numeric()),
         contains="AbstractMassObject")

## overwrite default validation method (checks for non-empty intensity etc)
## needs to be rewritten obviously
.validAbstractMassObject <- function(object) {
  TRUE
}
setValidity("AbstractMassObject", method=.validAbstractMassObject)

createMassSpectrumOnDisk <- function(mass, intensity, metaData=list()) {
    object <- new("MassSpectrumOnDisk",
        mass=numeric(), intensity=numeric(), n=length(mass), metaData=metaData,
        path=setNames(
            paste(
                tempfile("spectrum"), c("mass", "intensity"), sep="."),
                c("mass", "intensity")
        )
    )
    mass(object) <- mass
    intensity(object) <- intensity
    object
}

setMethod(f="show",
          signature=signature(object="MassSpectrumOnDisk"),
          definition=function(object) {
    callNextMethod()
    cat("Path:", object@path, sep="\n")

})

setMethod(f="mass",
          signature=signature(object="MassSpectrumOnDisk"),
          definition=function(object, ...) {
    readBin(object@path["mass"], "double", object@n)
})

setReplaceMethod(f="mass",
          signature=signature(object="MassSpectrumOnDisk", value="numeric"),
          definition=function(object, value) {

  if (length(value) == object@n) {
    writeBin(as.double(value), object@path["mass"])
  } else {
    stop("Lengths of mass (", object@n, ") and value (",
         length(value), ") have to be equal.")
  }
  object
})

setMethod(f="intensity",
          signature=signature(object="MassSpectrumOnDisk"),
          definition=function(object, ...) {
    readBin(object@path["intensity"], "double", object@n)
})

setReplaceMethod(f="intensity",
          signature=signature(object="MassSpectrumOnDisk", value="numeric"),
          definition=function(object, value) {

  if (length(value) == object@n) {
    writeBin(as.double(value), object@path["intensity"])
  } else {
    stop("Lengths of intensity (", object@n, ") and value (",
         length(value), ") have to be equal.")
  }
  object
})

s <- createMassSpectrumOnDisk(1:10, 1:10)
# S4 class type            : MassSpectrumOnDisk
# Number of m/z values     : 10                
# Range of m/z values      : 1 - 10            
# Range of intensity values: 1e+00 - 1e+01     
# Memory usage             : 1.805 KiB         
# Path:
# /tmp/RtmpyVT7vx/spectrum1f7f67cbd33d.mass
# /tmp/RtmpyVT7vx/spectrum1f7f67cbd33d.intensity
s
mass(s)
intensity(s)
intensity(s) <- 11:20
intensity(s)