Nothing
setClass("MassArrayPeak",
representation(
ID = "integer",
MW.theoretical = "numeric",
MW.actual = "numeric",
probability = "numeric",
SNR = "numeric",
height = "numeric",
sample.intensity = "numeric",
ref.intensity = "numeric",
sequence = "character",
adduct = "character",
type = "character",
charge = "integer",
collisions = "integer",
components = "integer",
missing = "logical",
new = "logical"
),
prototype(
ID = as.integer(-1),
MW.theoretical = as.numeric(0),
MW.actual = as.numeric(0),
probability = as.numeric(0),
SNR = as.numeric(0),
height = as.numeric(0),
sample.intensity = as.numeric(0),
ref.intensity = as.numeric(0),
sequence = "",
adduct = "",
type = "",
charge = as.integer(0),
collisions = as.integer(0),
components = as.integer(0),
missing = FALSE,
new = FALSE
)
)
setMethod("initialize",
"MassArrayPeak",
function(.Object,
ID,
MW.theoretical = as.numeric(0),
MW.actual = as.numeric(0),
probability = as.numeric(0),
SNR = as.numeric(0),
height = as.numeric(0),
sample.intensity = as.numeric(0),
ref.intensity = as.numeric(0),
sequence = "",
adduct = c("", "Na", "K"),
type = c("Expected", "Modified", "Unknown", "Control"),
charge = as.integer(1),
collisions = as.integer(0),
components = as.integer(0),
missing = FALSE,
new = FALSE,
...
) {
.Object@ID <- as.integer(ID)
.Object@MW.theoretical <- as.numeric(MW.theoretical)
.Object@MW.actual <- as.numeric(MW.actual)
.Object@probability <- as.numeric(probability)
.Object@SNR <- as.numeric(SNR)
.Object@height <- as.numeric(height)
.Object@sample.intensity <- as.numeric(sample.intensity)
.Object@ref.intensity <- as.numeric(ref.intensity)
.Object@sequence <- as.character(toupper(sequence))
.Object@adduct <- match.arg(adduct)
.Object@type <- match.arg(type)
.Object@charge <- as.integer(charge)
.Object@collisions <- as.integer(collisions)
.Object@components <- as.integer(components)
.Object@missing <- missing
.Object@new <- new
return(.Object)
}
)
setValidity("MassArrayPeak",
function(object) {
return(TRUE)
}
)
setMethod("$", "MassArrayPeak",
function (x, name) {
if (inherits(try(slot(x, name), silent=TRUE), "try-error")) {
return(NULL)
}
else {
return(slot(x, name))
}
}
)
setMethod("$<-", "MassArrayPeak",
function (x, name, value) {
if (inherits(try(slot(x, name), silent=TRUE), "try-error")) {
warning("'", name, "' is not a parameter in class 'MassArrayPeak'")
}
else {
slot(x, name) <- value
}
return(x)
}
)
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