R/spectra_ref.R

In lifs-tools/rmzTab-m: R Package Client for mzTab-M Reference Implementation and Validation API

# mzTab-M reference implementation and validation API.
#
# This is the mzTab-M reference implementation and validation API service.
#
# The version of the OpenAPI document: 2.0.0
# Contact: nils.hoffmann@cebitec.uni-bielefeld.de
# Generated by: https://openapi-generator.tech

#' @docType class
#' @title SpectraRef
#' @description SpectraRef Class
#' @format An \code{R6Class} generator object
#' @field ms_run  \link{MsRun} 
#'
#' @field reference  character 
#'
#'
#' @importFrom R6 R6Class
#' @importFrom jsonlite fromJSON toJSON
#' @export
SpectraRef <- R6::R6Class(
  'SpectraRef',
  public = list(
    `ms_run` = NULL,
    `reference` = NULL,
    #' @description Create a SpectraRef
    #' @param ms_run The ms run \link{MsRun} .
    #' @param reference The reference to a particular spectrum using the id_format defined in \link{MsRun}.
    #' @param ... local optional variable arguments
    #'     
    initialize = function(`ms_run`, `reference`, ...){
      local.optional.var <- list(...)
      if (!missing(`ms_run`)) {
        stopifnot(is.numeric(`ms_run`), length(`ms_run`) == 1)
        self$`ms_run` <- `ms_run`
      }
      if (!missing(`reference`)) {
        stopifnot(is.character(`reference`), length(`reference`) == 1)
        self$`reference` <- `reference`
      }
    },
    #' @description Serialize to list object suitable for jsonlite
    toJSON = function() {
      SpectraRefObject <- list()
      if (!is.null(self$`ms_run`)) {
        SpectraRefObject[['ms_run']] <-
          rmzTabM::safe_unbox(self$`ms_run`)
      }
      if (!is.null(self$`reference`)) {
        SpectraRefObject[['reference']] <-
          rmzTabM::safe_unbox(self$`reference`)
      }

      SpectraRefObject
    },
    #' @description Deserialize from jsonlite list object
    #' @param SpectraRefJson list object.
    fromJSON = function(SpectraRefJson) {
      SpectraRefObject <- jsonlite::fromJSON(SpectraRefJson)
      if (!is.null(SpectraRefObject$`ms_run`)) {
        self$`ms_run` <- SpectraRefObject$`ms_run`
      }
      if (!is.null(SpectraRefObject$`reference`)) {
        self$`reference` <- SpectraRefObject$`reference`
      }
    },
    #' @description Serialize to JSON string.
    toJSONString = function() {
      jsoncontent <- c(
        if (!is.null(self$`ms_run`)) {
        sprintf(
        '"ms_run":
        %d
        ',
        rmzTabM::safe_unbox(self$`ms_run`)
        )},
        if (!is.null(self$`reference`)) {
        sprintf(
        '"reference":
          "%s"
                ',
        rmzTabM::safe_unbox(self$`reference`)
        )}
      )
      jsoncontent <- paste(jsoncontent, collapse = ",")
      paste('{', jsoncontent, '}', sep = "")
    },
    #' @description Deserialize from JSON string
    #' @param SpectraRefJson JSON string
    fromJSONString = function(SpectraRefJson) {
      SpectraRefObject <- jsonlite::fromJSON(SpectraRefJson)
      self$`ms_run` <- MsRun$new()$fromJSONString(jsonlite::toJSON(SpectraRefObject$ms_run, auto_unbox = TRUE, null = "null", na = "null", digits = NA))
      self$`reference` <- SpectraRefObject$`reference`
      self
    },
    #' @description Serialize to string
    toString = function() {
      spectraRefStr <- ""
      if (!is.null(self$`ms_run`) && !is.null(self$`reference`)) {
        if (typeof(self$`ms_run`)=="double" || typeof(self$`ms_run`)=="integer") {
          spectraRefStr <- paste0("ms_run[", self$`ms_run`, "]:", self$`reference`)
        } else {
          spectraRefStr <- paste0("ms_run[", self$`ms_run`$`id`, "]:", self$`reference`)
        }
      }
      spectraRefStr
    },
    #' @description Deerialize from string
    #' @param SpectraRefString The SpectraRef string representation.
    fromString = function(SpectraRefString) {
      split <- strsplit(SpectraRefString, ":", fixed=TRUE)
      self$`ms_run` <- extractId(split[[1]][[1]], regexp = idElementRegexp)
      self$`reference` <- split[[1]][[2]]
      self
    }
  )
)