Fix set_energy<- so that argument value appears at the end of the arg…

…ument list

NEWS.md

@@ -1,6 +1,7 @@
 # gamma 1.0.3.9000
 ## Bugfixes & changes
 * Fix the metadata when reading a CNF file: do not use a fixed index to isolate particular metadata (the number of metadata may vary depending on the user's acquisition).
+* Fix `set_energy<-` so that argument `value` appears in the method at the end of the argument list.
 
 # gamma 1.0.3
 ## Bugfixes & changes

R/AllGenerics.R

@@ -26,7 +26,8 @@ NULL
 #' Getters and setters to extract or replace parts of an object.
 #' @param x An object from which to get or set element(s).
 #' @param value A possible value for the element(s) of `x`.
-#' @param expected TODO.
+#' @param expected A [`logical`] scalar: should the expected values be returned
+#'  instead of observed values?
 #' @param na.rm A [`logical`] scalar: should [`NA`] be omitted?
 #' @param ... Currently not used.
 #' @return
@@ -106,7 +107,7 @@ setGeneric(
 #' @aliases set_energy-method
 setGeneric(
   name = "set_energy<-",
-  def = function(x, ..., value) standardGeneric("set_energy<-")
+  def = function(x, value) standardGeneric("set_energy<-")
 )
 
 #' @rdname mutator

R/mutators.R

@@ -231,7 +231,7 @@ setMethod(
   signature = "GammaSpectra",
   definition = function(x, na.rm = FALSE) {
     channels <- vapply(x, FUN = range_channels, FUN.VALUE = numeric(2),
-                      na.rm = na.rm)
+                       na.rm = na.rm)
     channels <- t(channels)
     colnames(channels) <- c("min", "max")
     channels
@@ -358,17 +358,12 @@ setMethod(
 setMethod(
   f = "set_energy<-",
   signature = c(x = "PeakPosition", value = "numeric"),
-  definition = function(x, value, expected = TRUE) {
+  definition = function(x, value) {
     # Keep only complete cases
     k <- if (anyNA(value)) which(!is.na(value)) else seq_along(value)
 
-    if (expected) {
-      x@energy_expected <- value[k]
-      x@energy_observed <- x@energy_observed[k]
-    } else {
-      x@energy_observed <- value[k]
-      x@energy_expected <- x@energy_expected[k]
-    }
+    x@energy_observed <- x@energy_observed[k]
+    x@energy_expected <- value[k]
     x@channel <- x@channel[k]
     methods::validObject(x)
     x