R/allClasses.R

In msettles/rSFFreader: rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers

.sffValidity <- function(object) TRUE
setGeneric(".sffValidity")

## Classes
setClass("SffHeader", contains=c(),
         representation=representation(
           header="list"),
         prototype=prototype(
           header=list())
)

setClass("SffReads", contains="SffHeader",
         representation = representation(
	         sread="DNAStringSet",
           qualityIR="IRanges",
           adapterIR="IRanges",
           customIR="IRanges",
           clipMode="character"),
         prototype=prototype(
	       sread=DNAStringSet(character(0)),
           qualityIR=IRanges(),
           adapterIR=IRanges(),
           customIR=IRanges(),
           clipMode="Full"),
         validity=.sffValidity
)

setClass("SffReadsQ", contains="SffReads",
         representation=representation(
           quality="QualityScore"),
         prototype=prototype(
           quality=NumericQuality()),
         validity=.sffValidity
)

setClass("SffReadsF", contains="SffReadsQ",
         representation=representation(
           flowgram="matrix",
           flowindices="list"),
         prototype=prototype(
           flowgram=matrix(numeric(0)),
           flowindices=list(numeric(0))),
         validity=.sffValidity         
)