Nothing
# modification on git from copied files
setMethod("c", "lociData", function(x, ..., recursive = FALSE) {
cdl <- list(...)
catLD <- callNextMethod()
if(all(sapply(cdl, function(z) all.equal(z@replicates, current = x@replicates)))) {
nLL <- do.call("rbind", (c(list(x@locLikelihoods), lapply(cdl, function(x) x@locLikelihoods))))
}
nCoord <- do.call("c", c(list(x@coordinates), lapply(cdl, function(x) x@coordinates)))
new("lociData", catLD, locLikelihoods = nLL, coordinates = nCoord)
})
setMethod("show", "lociData", function(object) {
show(object@coordinates)
callNextMethod()
.printLocLikes(object@locLikelihoods)
if(nrow(object@locLikelihoods) > 0) {
cat("\nExpected number of loci in each replicate group\n")
print(colSums(exp(object@locLikelihoods)))
}
})
setMethod("[", "lociData", function(x, i, j, ..., drop = FALSE) {
if(missing(j))
j <- 1:ncol(x@data)
if(missing(i))
i <- 1:nrow(x@data)
if(length(i) == 0) return(x)
i <- as.vector(i)
j <- as.vector(j)
x <- callNextMethod()
if(nrow(x@locLikelihoods) > 0)
x@locLikelihoods <- x@locLikelihoods[i,, drop = FALSE]
if(length(x@coordinates) > 0)
x@coordinates <- x@coordinates[i,, drop = FALSE]
x
})
setMethod("dim", "lociData", function(x) {
dim <- dim(x@data)
if(dim[1] == 0) dim[1] <- length(x@coordinates)
dim
})
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