R/segClass-accessors.R

In segmentSeq: Methods for identifying small RNA loci from high-throughput sequencing data

# modification on git from copied files
#setMethod("[", "segClass", function(x, i, j, ..., drop = FALSE) {
#  if(!missing(i))
#    {
#      i <- as.vector(i)
#      x@coordinates <- x@coordinates[i,,drop = FALSE]
#      if(nrow(x@locLikelihoods) > 0)
#        x@locLikelihoods <- x@locLikelihoods[i,,drop = FALSE]
#    }
#
#  if(!missing(j))
#    {
#      j <- as.vector(j)
#      x@replicates <- x@replicates[j]
#    }  
#  x
#})

#setMethod("dim", "segClass", function(x) {
#  c(max(length(x@coordinates), nrow(x@locLikelihoods)), length(x@replicates))
#})


#setMethod("show", "segClass", function(object) {
#  cat(paste('An object of class "', class(object), '"\n', sep = ""))
#  cat(paste(nrow(object), 'rows and', ncol(object), 'columns\n'))
#  cat('\nSlot "replicates":\n')
#  print(object@replicates)
#  cat('\nSlot "coordinates":\n')
#  print(object@coordinates)
#  .printLocLikes(object@locLikelihoods)
#})