R/Containertype.R

In BigelowLab/genologicsr: A simplified interface between XML nodes and the Genologics RESTful API

# Containertype.R

#' A Containertype representation that subclasses from NodeRefClass
#' 
#' @family Node
#' @field name character, name if any
#' @field is_tube logical, type if any
#' @field xdim, list [is_alpha = TRUE/FALSE, offset = 0/1, size = n]
#' @field ydim, list [is_alpha = TRUE/FALSE, offset = 0/1, size = n]
#' @include Node.R
#' @export
ContainerTypeRefClass <- setRefClass("ContainerTypeRefClass",
   contains = "NodeRefClass",
   fields = list(
      name = 'character',
      is_tube = 'logical',
      xdim = 'list',
      ydim = 'list'),
   methods = list(
    show = function(prefix = ""){
       callSuper(prefix = prefix)
       cat(prefix, "  Container type name: ", .self$name, "\n", sep = "")
       cat(prefix, "  Container type is_tube: ", .self$is_tube, "\n", sep = "")
       cat(prefix, "  Container type width: ", .self$xdim[["size"]], "\n", sep = "")
       cat(prefix, "  Container type height: ", .self$ydim[["size"]], "\n", sep = "")
    },
    get_dim = function(what = 'x'){
       what = paste0(tolower(what[1]), "-dimension")
       x <- .self$node[[what]]
       list(
          is_alpha = xml_value(x[['is-alpha']]) == "true",
          offset = as.numeric(xml_value(x[['offset']])),
          size = as.numeric(xml_value(x[['size']])))
    },
    test_if_tube = function(){
       if (.self$lims$version == 'v1'){
          istube <- (.self$xdim[['size']] * .self$ydim[['size']]) == 1
       } else {
          istube <- xml_value(.self$node[['is-tube']]) == 'true'
       }
       return(istube)
    },      
    initialize = function(...){
       callSuper(...)
       .self$verbs <- c("GET", "BROWSE")
    
    },
    update = function(...){
        callSuper(...)
        .self$name = xml_atts(.self$node)[['name']]
        .self$xdim = .self$get_dim(what="x")
        .self$ydim = .self$get_dim(what="y")
        .self$is_tube = .self$test_if_tube() 
    } 
      ) # methods
      
   ) #setRefClass