strvalidator: Process Control and Validation of Forensic STR Kits

Documented in calculateResultType_gui

###############################################################################
# CHANGE LOG (last 20 changes)
# 08.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 07.03.2020: Added language support.
# 23.03.2019: Fixed Error in paste(parent$ID, parent$env$num.subwin... (tcltk)
# 17.02.2019: Fixed Error in if (svalue(savegui_chk)) { : argument is of length zero (tcltk)
# 07.08.2017: Added audit trail.
# 13.07.2017: Fixed issue with button handlers.
# 13.07.2017: Fixed narrow dropdown with hidden argument ellipsize = "none".
# 07.07.2017: Replaced 'droplist' with 'gcombobox'.
# 07.07.2017: Removed argument 'border' for 'gbutton'.
# 18.09.2016: Added attributes to result.
# 29.04.2016: 'Save as' textbox expandable.
# 28.08.2015: Added importFrom.
# 04.06.2015: Changed button label 'Calculate result type' to 'Calculate'.
# 11.10.2014: Added 'focus', added 'parent' parameter.
# 28.06.2014: Added help button and moved save gui checkbox.
# 08.05.2014: Implemented 'checkDataset'.
# 15.01.2014: Added option for parameter to add missing markers.
# 10.11.2013: Added kit dropbox.
# 03.11.2013: First version.

#' @title Calculate Result Type
#'
#' @description
#' GUI wrapper for the \code{\link{calculateResultType}} function.
#'
#' @details Simplifies the use of \code{\link{calculateResultType}} by providing a
#' graphical user interface.
#'
#' @param env environment in which to search for data frames and save result.
#' @param savegui logical indicating if GUI settings should be saved in the environment.
#' @param debug logical indicating printing debug information.
#' @param parent widget to get focus when finished.
#'
#' @export
#'
#' @importFrom utils help
#'
#' @return TRUE
#'
#' @seealso \code{\link{calculateResultType}}

calculateResultType_gui <- function(env = parent.frame(), savegui = NULL,
                                    debug = FALSE, parent = NULL) {
  # Global variables.
  .gData <- NULL
  .gDataName <- NULL

  # Language ------------------------------------------------------------------

  # Get this functions name from call.
  fnc <- as.character(match.call()[[1]])

  if (debug) {
    print(paste("IN:", fnc))
  }

  # Default strings.
  strWinTitle <- "Calculate result type"
  strChkGui <- "Save GUI settings"
  strBtnHelp <- "Help"
  strFrmDataset <- "Dataset and kit"
  strLblDataset <- "Sample dataset:"
  strDrpDataset <- "<Select dataset>"
  strLblSamples <- "samples"
  strLblKit <- "Kit:"
  strFrmOptions <- "Options"
  strLblNB <- "NB! All markers must be present in each sample for correct results."
  strLblPre <- "Pre-processing:"
  strChkMissing <- "Add missing markers (can be slow on large datasets)"
  strLblMethod <- "Calculate result type:"
  strLblHeight <- "Define subtypes of complete profiles by all peaks > peak height threshold (RFU):"
  strTipHeight <- "Complete >[RFU]"
  strLblMarker <- "Define subtypes of mixtures by number of markers with > 2 detected peaks:"
  strTipMarker <- "Mixture >[markers]"
  strLblPeak <- "Define subtypes of partial profiles by number of detected peaks:"
  strTipPeak <- "Partial >[peaks]"
  strLblFullKit <- "Define subtypes of partial profiles by kit:"
  strDrpKit <- "<Select kit>"
  strTipFullKit <- "Partial Complete [kit]"
  strFrmSave <- "Save as"
  strLblSave <- "Name for result:"
  strBtnCalculate <- "Calculate"
  strBtnProcessing <- "Processing..."
  strMsgDataset <- "A sample dataset must be selected."
  strMsgTitleDataset <- "Dataset not selected"

  # Get strings from language file.
  dtStrings <- getStrings(gui = fnc)

  # If language file is found.
  if (!is.null(dtStrings)) {
    # Get language strings, use default if not found.

    strtmp <- dtStrings["strWinTitle"]$value
    strWinTitle <- ifelse(is.na(strtmp), strWinTitle, strtmp)

    strtmp <- dtStrings["strChkGui"]$value
    strChkGui <- ifelse(is.na(strtmp), strChkGui, strtmp)

    strtmp <- dtStrings["strBtnHelp"]$value
    strBtnHelp <- ifelse(is.na(strtmp), strBtnHelp, strtmp)

    strtmp <- dtStrings["strFrmDataset"]$value
    strFrmDataset <- ifelse(is.na(strtmp), strFrmDataset, strtmp)

    strtmp <- dtStrings["strLblDataset"]$value
    strLblDataset <- ifelse(is.na(strtmp), strLblDataset, strtmp)

    strtmp <- dtStrings["strDrpDataset"]$value
    strDrpDataset <- ifelse(is.na(strtmp), strDrpDataset, strtmp)

    strtmp <- dtStrings["strLblSamples"]$value
    strLblSamples <- ifelse(is.na(strtmp), strLblSamples, strtmp)

    strtmp <- dtStrings["strLblKit"]$value
    strLblKit <- ifelse(is.na(strtmp), strLblKit, strtmp)

    strtmp <- dtStrings["strFrmOptions"]$value
    strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)

    strtmp <- dtStrings["strLblNB"]$value
    strLblNB <- ifelse(is.na(strtmp), strLblNB, strtmp)

    strtmp <- dtStrings["strLblPre"]$value
    strLblPre <- ifelse(is.na(strtmp), strLblPre, strtmp)

    strtmp <- dtStrings["strChkMissing"]$value
    strChkMissing <- ifelse(is.na(strtmp), strChkMissing, strtmp)

    strtmp <- dtStrings["strLblMethod"]$value
    strLblMethod <- ifelse(is.na(strtmp), strLblMethod, strtmp)

    strtmp <- dtStrings["strLblHeight"]$value
    strLblHeight <- ifelse(is.na(strtmp), strLblHeight, strtmp)

    strtmp <- dtStrings["strTipHeight"]$value
    strTipHeight <- ifelse(is.na(strtmp), strTipHeight, strtmp)

    strtmp <- dtStrings["strLblMarker"]$value
    strLblMarker <- ifelse(is.na(strtmp), strLblMarker, strtmp)

    strtmp <- dtStrings["strTipMarker"]$value
    strTipMarker <- ifelse(is.na(strtmp), strTipMarker, strtmp)

    strtmp <- dtStrings["strLblPeak"]$value
    strLblPeak <- ifelse(is.na(strtmp), strLblPeak, strtmp)

    strtmp <- dtStrings["strTipPeak"]$value
    strTipPeak <- ifelse(is.na(strtmp), strTipPeak, strtmp)

    strtmp <- dtStrings["strLblFullKit"]$value
    strLblFullKit <- ifelse(is.na(strtmp), strLblFullKit, strtmp)

    strtmp <- dtStrings["strTipFullKit"]$value
    strTipFullKit <- ifelse(is.na(strtmp), strTipFullKit, strtmp)

    strtmp <- dtStrings["strDrpKit"]$value
    strDrpKit <- ifelse(is.na(strtmp), strDrpKit, strtmp)

    strtmp <- dtStrings["strFrmSave"]$value
    strFrmSave <- ifelse(is.na(strtmp), strFrmSave, strtmp)

    strtmp <- dtStrings["strLblSave"]$value
    strLblSave <- ifelse(is.na(strtmp), strLblSave, strtmp)

    strtmp <- dtStrings["strBtnCalculate"]$value
    strBtnCalculate <- ifelse(is.na(strtmp), strBtnCalculate, strtmp)

    strtmp <- dtStrings["strBtnProcessing"]$value
    strBtnProcessing <- ifelse(is.na(strtmp), strBtnProcessing, strtmp)

    strtmp <- dtStrings["strMsgDataset"]$value
    strMsgDataset <- ifelse(is.na(strtmp), strMsgDataset, strtmp)

    strtmp <- dtStrings["strMsgTitleDataset"]$value
    strMsgTitleDataset <- ifelse(is.na(strtmp), strMsgTitleDataset, strtmp)
  }

  # WINDOW ####################################################################

  # Main window.
  w <- gwindow(title = strWinTitle, visible = FALSE)

  # Runs when window is closed.
  addHandlerUnrealize(w, handler = function(h, ...) {
    # Save GUI state.
    .saveSettings()

    # Focus on parent window.
    if (!is.null(parent)) {
      focus(parent)
    }

    # Destroy window.
    return(FALSE)
  })

  # Vertical main group.
  gv <- ggroup(
    horizontal = FALSE,
    spacing = 1,
    use.scrollwindow = FALSE,
    container = w,
    expand = TRUE
  )

  # Help button group.
  gh <- ggroup(container = gv, expand = FALSE, fill = "both")

  savegui_chk <- gcheckbox(text = strChkGui, checked = FALSE, container = gh)

  addSpring(gh)

  help_btn <- gbutton(text = strBtnHelp, container = gh)

  addHandlerChanged(help_btn, handler = function(h, ...) {
    # Open help page for function.
    print(help(fnc, help_type = "html"))
  })

  # FRAME 0 ###################################################################

  f0 <- gframe(
    text = strFrmDataset,
    horizontal = FALSE,
    spacing = 1,
    container = gv
  )

  # Datasets ------------------------------------------------------------------

  g0 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")

  glabel(text = strLblDataset, container = g0)

  samples_lbl <- glabel(
    text = paste(" 0", strLblSamples),
    container = g0
  )

  dataset_drp <- gcombobox(
    items = c(
      strDrpDataset,
      listObjects(
        env = env,
        obj.class = "data.frame"
      )
    ),
    selected = 1,
    editable = FALSE,
    container = g0,
    ellipsize = "none",
    expand = TRUE,
    fill = "x"
  )

  # Kit -----------------------------------------------------------------------

  g1 <- ggroup(container = f0, spacing = 1, expand = TRUE, fill = "x")

  glabel(text = strLblKit, container = g1)

  kit_drp <- gcombobox(
    items = getKit(),
    selected = 1,
    editable = FALSE,
    container = g1,
    ellipsize = "none",
    expand = TRUE,
    fill = "x"
  )

  addHandlerChanged(dataset_drp, handler = function(h, ...) {
    val_obj <- svalue(dataset_drp)

    # Check if suitable.
    requiredCol <- c("Sample.Name", "Marker", "Allele", "Height")
    ok <- checkDataset(
      name = val_obj, reqcol = requiredCol,
      env = env, parent = w, debug = debug
    )

    if (ok) {
      # Load or change components.
      .gData <<- get(val_obj, envir = env)
      .gDataName <<- val_obj
      samples <- length(unique(.gData$Sample.Name))
      svalue(samples_lbl) <- paste("", samples, strLblSamples)
      svalue(save_edt) <- paste(val_obj, "_type", sep = "")

      # Detect kit.
      kitIndex <- detectKit(.gData, index = TRUE)
      # Select in dropdown.
      svalue(kit_drp, index = TRUE) <- kitIndex
    } else {
      # Reset components.
      .gData <<- NULL
      .gDataName <<- NULL
      svalue(dataset_drp, index = TRUE) <- 1
      svalue(samples_lbl) <- paste(" 0", strLblSamples)
      svalue(save_edt) <- ""
    }
  })

  # FRAME 1 ###################################################################

  f1 <- gframe(
    text = strFrmOptions,
    horizontal = FALSE,
    spacing = 1,
    container = gv
  )

  glabel(text = strLblNB, container = f1, anchor = c(-1, 0))

  glabel(text = strLblPre, container = f1, anchor = c(-1, 0))

  f1_add_chk <- gcheckbox(text = strChkMissing, checked = TRUE, container = f1)

  glabel(text = strLblMethod, container = f1, anchor = c(-1, 0))

  glabel(text = strLblHeight, container = f1, anchor = c(-1, 0))

  f1_rfu_edt <- gedit(text = "", width = 6, container = f1)
  tooltip(f1_rfu_edt) <- strTipHeight

  glabel(text = strLblMarker, container = f1, anchor = c(-1, 0))

  f1_mix_edt <- gedit(text = "", width = 6, container = f1)
  tooltip(f1_mix_edt) <- strTipMarker

  glabel(text = strLblPeak, container = f1, anchor = c(-1, 0))

  f1_par_edt <- gedit(text = "", width = 6, container = f1)
  tooltip(f1_par_edt) <- strTipPeak

  glabel(text = strLblFullKit, container = f1, anchor = c(-1, 0))

  f1_kit_drp <- gcombobox(
    items = c(strDrpKit, getKit()),
    selected = 1,
    editable = FALSE,
    container = f1,
    ellipsize = "none"
  )

  # SAVE ######################################################################

  save_frame <- gframe(text = strFrmSave, container = gv)

  glabel(text = strLblSave, container = save_frame)

  save_edt <- gedit(expand = TRUE, fill = TRUE, container = save_frame)

  # BUTTON ####################################################################


  calculate_btn <- gbutton(text = strBtnCalculate, container = gv)

  addHandlerClicked(calculate_btn, handler = function(h, ...) {
    val_data <- .gData
    val_name_data <- .gDataName
    val_threshold <- as.numeric(svalue(f1_rfu_edt))
    val_mix <- svalue(f1_mix_edt)
    val_par <- svalue(f1_par_edt)
    val_subkit <- svalue(f1_kit_drp)
    val_name <- svalue(save_edt)
    val_marker <- NULL
    val_kit <- svalue(kit_drp)
    val_add <- svalue(f1_add_chk)

    if (debug) {
      print("GUI options:")
      print("val_threshold")
      print(val_threshold)
      print("val_mix")
      print(val_mix)
      print("val_par")
      print(val_par)
      print("val_subkit")
      print(val_subkit)
      print("val_marker")
      print(val_marker)
      print("val_name")
      print(val_name)
      print("val_kit")
      print(val_kit)
      print("val_add")
      print(val_add)
    }

    # Prepare arguments -------------------------------------------------------

    # No threshold is represented by NULL.
    if (is.na(val_threshold)) {
      val_threshold <- NULL
    }

    # Check if empty.
    if (nchar(val_mix) == 0) {
      # No limit is represented by NULL.
      val_mix <- NULL
    } else {
      # Convert string to numeric vector.
      val_mix <- unlist(strsplit(x = val_mix, split = ",", fixed = TRUE))
      val_mix <- as.numeric(val_mix)
    }

    # Check if empty.
    if (nchar(val_par) == 0) {
      # No limit is represented by NULL.
      val_par <- NULL
    } else {
      # Convert string to numeric vector.
      val_par <- unlist(strsplit(x = val_par, split = ",", fixed = TRUE))
      val_par <- as.numeric(val_par)
    }

    # Check if kit is provided and available.
    if (val_subkit %in% getKit()) {
      # Get marker names and create string.
      val_marker <- paste(getKit(kit = val_subkit, what = "Marker"), collapse = "|")
    } else {
      # Set to NA.
      val_subkit <- NA
    }

    if (debug) {
      print("Function arguments:")
      print("val_threshold")
      print(val_threshold)
      print("val_mix")
      print(val_mix)
      print("val_par")
      print(val_par)
      print("val_subkit")
      print(val_subkit)
      print("val_marker")
      print(val_marker)
      print("val_name")
      print(val_name)
      print("val_kit")
      print(val_kit)
    }

    if (!is.null(val_data)) {
      # Change button.
      blockHandlers(calculate_btn)
      svalue(calculate_btn) <- strBtnProcessing
      unblockHandlers(calculate_btn)
      enabled(calculate_btn) <- FALSE

      datanew <- calculateResultType(
        data = val_data,
        kit = val_kit,
        add.missing.marker = val_add,
        threshold = val_threshold,
        mixture.limits = val_mix,
        partial.limits = val_par,
        subset.name = val_subkit,
        marker.subset = val_marker,
        debug = debug
      )

      # Add attributes to result.
      attr(datanew, which = "kit") <- val_kit

      # Create key-value pairs to log.
      keys <- list(
        "data", "add.missing.marker", "threshold", "mixture.limits",
        "partial.limits", "subset.name", "marker.subset"
      )

      values <- list(
        val_name_data, val_add, val_threshold, val_mix,
        val_par, val_subkit, val_marker
      )

      # Update audit trail.
      datanew <- auditTrail(
        obj = datanew, key = keys, value = values,
        label = fnc,
        arguments = FALSE, package = "strvalidator"
      )

      # Save data.
      saveObject(name = val_name, object = datanew, parent = w, env = env)

      if (debug) {
        print(paste("EXIT:", fnc))
      }

      # Close GUI.
      .saveSettings()
      dispose(w)
    } else {
      gmessage(
        msg = strMsgDataset,
        title = strMsgTitleDataset,
        icon = "error",
        parent = w
      )
    }
  })

  # INTERNAL FUNCTIONS ########################################################

  .loadSavedSettings <- function() {
    # First check status of save flag.
    if (!is.null(savegui)) {
      svalue(savegui_chk) <- savegui
      enabled(savegui_chk) <- FALSE
      if (debug) {
        print("Save GUI status set!")
      }
    } else {
      # Load save flag.
      if (exists(".strvalidator_calculateResultType_gui_savegui", envir = env, inherits = FALSE)) {
        svalue(savegui_chk) <- get(".strvalidator_calculateResultType_gui_savegui", envir = env)
      }
      if (debug) {
        print("Save GUI status loaded!")
      }
    }
    if (debug) {
      print(svalue(savegui_chk))
    }

    # Then load settings if true.
    if (svalue(savegui_chk)) {
      if (exists(".strvalidator_calculateResultType_gui_rfu", envir = env, inherits = FALSE)) {
        svalue(f1_rfu_edt) <- get(".strvalidator_calculateResultType_gui_rfu", envir = env)
      }
      if (exists(".strvalidator_calculateResultType_gui_mix", envir = env, inherits = FALSE)) {
        svalue(f1_mix_edt) <- get(".strvalidator_calculateResultType_gui_mix", envir = env)
      }
      if (exists(".strvalidator_calculateResultType_gui_par", envir = env, inherits = FALSE)) {
        svalue(f1_par_edt) <- get(".strvalidator_calculateResultType_gui_par", envir = env)
      }
      if (exists(".strvalidator_calculateResultType_gui_kit", envir = env, inherits = FALSE)) {
        svalue(f1_kit_drp) <- get(".strvalidator_calculateResultType_gui_kit", envir = env)
      }
      if (exists(".strvalidator_calculateResultType_gui_add", envir = env, inherits = FALSE)) {
        svalue(f1_add_chk) <- get(".strvalidator_calculateResultType_gui_add", envir = env)
      }

      if (debug) {
        print("Saved settings loaded!")
      }
    }
  }

  .saveSettings <- function() {
    # Then save settings if true.
    if (svalue(savegui_chk)) {
      assign(x = ".strvalidator_calculateResultType_gui_savegui", value = svalue(savegui_chk), envir = env)
      assign(x = ".strvalidator_calculateResultType_gui_rfu", value = svalue(f1_rfu_edt), envir = env)
      assign(x = ".strvalidator_calculateResultType_gui_mix", value = svalue(f1_mix_edt), envir = env)
      assign(x = ".strvalidator_calculateResultType_gui_par", value = svalue(f1_par_edt), envir = env)
      assign(x = ".strvalidator_calculateResultType_gui_kit", value = svalue(f1_kit_drp), envir = env)
      assign(x = ".strvalidator_calculateResultType_gui_add", value = svalue(f1_add_chk), envir = env)
    } else { # or remove all saved values if false.

      if (exists(".strvalidator_calculateResultType_gui_savegui", envir = env, inherits = FALSE)) {
        remove(".strvalidator_calculateResultType_gui_savegui", envir = env)
      }
      if (exists(".strvalidator_calculateResultType_gui_rfu", envir = env, inherits = FALSE)) {
        remove(".strvalidator_calculateResultType_gui_rfu", envir = env)
      }
      if (exists(".strvalidator_calculateResultType_gui_mix", envir = env, inherits = FALSE)) {
        remove(".strvalidator_calculateResultType_gui_mix", envir = env)
      }
      if (exists(".strvalidator_calculateResultType_gui_par", envir = env, inherits = FALSE)) {
        remove(".strvalidator_calculateResultType_gui_par", envir = env)
      }
      if (exists(".strvalidator_calculateResultType_gui_kit", envir = env, inherits = FALSE)) {
        remove(".strvalidator_calculateResultType_gui_kit", envir = env)
      }
      if (exists(".strvalidator_calculateResultType_gui_add", envir = env, inherits = FALSE)) {
        remove(".strvalidator_calculateResultType_gui_add", envir = env)
      }

      if (debug) {
        print("Settings cleared!")
      }
    }

    if (debug) {
      print("Settings saved!")
    }
  }

  # END GUI ###################################################################

  # Load GUI settings.
  .loadSavedSettings()

  # Show GUI.
  visible(w) <- TRUE
  focus(w)
}