Nothing
################################################################################
# CHANGE LOG (last 20 changes)
# 05.09.2022: Compacted gui. Removed destroy workaround.
# 03.03.2020: Added language support.
# 03.03.2020: Expand scrollable checkbox view.
# 19.02.2019: Expand text field under tcltk. Scrollable checkbox view.
# 17.02.2019: Fixed Error in if (svalue(savegui_chk)) { : argument is of length zero (tcltk)
# 06.08.2017: 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'.
# 28.08.2015: Added importFrom
# 11.10.2014: Added 'focus', added 'parent' parameter.
# 28.06.2014: Added help button and moved save gui checkbox.
# 21.01.2014: Added parameter 'limit'.
# 06.01.2014: Fixed button name used as 'save as' name.
# 20.11.2013: Fixed result now stored in variable 'datanew' insted of 'val_name'.
# 29.09.2013: First version.
#' @title Analyze Off-ladder Alleles
#'
#' @description
#' GUI wrapper for the \code{\link{calculateOL}} function.
#'
#' @details By analysis of the allelic ladder the risk for getting off-ladder
#' (OL) alleles are calculated. The frequencies from a provided population
#' database is used to calculate the risk per marker and in total for the given
#' kit(s). Virtual alleles can be excluded from the calculation.
#' Small frequencies can be limited to the estimate 5/2N.
#'
#' @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.
#'
#' @return TRUE
#'
#' @export
#'
#' @importFrom utils help str
#'
#' @seealso \code{\link{calculateOL}}
calculateOL_gui <- function(env = parent.frame(), savegui = NULL, debug = TRUE, parent = NULL) {
# Language ------------------------------------------------------------------
# Get this functions name from call.
fnc <- as.character(match.call()[[1]])
if (debug) {
print(paste("IN:", fnc))
}
# Default strings.
strWinTitle <- "Analyse off-ladder alleles"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmKits <- "Select kits"
strFrmOptions <- "Options"
strLblDatabase <- "Select allele frequency database:"
strChkVirtual <- "Include virtual bins in analysis"
strTipVirtual <- "NB! Not all vendors specify which alleles are virtual in the bins file. This can be done manually in the kit.txt file."
strChkLowFreq <- "Limit small frequencies to 5/2N"
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strBtnCalculate <- "Calculate"
strBtnProcessing <- "Processing..."
strMsgKit <- "At least one kit must be selected."
strMsgTitleKit <- "No kit 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"]$value
strBtnHelp <- ifelse(is.na(strtmp), strBtnHelp, strtmp)
strtmp <- dtStrings["strFrmKits"]$value
strFrmKits <- ifelse(is.na(strtmp), strFrmKits, strtmp)
strtmp <- dtStrings["strFrmOptions"]$value
strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)
strtmp <- dtStrings["strLblDatabase"]$value
strLblDatabase <- ifelse(is.na(strtmp), strLblDatabase, strtmp)
strtmp <- dtStrings["strChkVirtual"]$value
strChkVirtual <- ifelse(is.na(strtmp), strChkVirtual, strtmp)
strtmp <- dtStrings["strTipVirtual"]$value
strTipVirtual <- ifelse(is.na(strtmp), strTipVirtual, 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["strMsgKit"]$value
strMsgKit <- ifelse(is.na(strtmp), strMsgKit, strtmp)
strtmp <- dtStrings["strMsgTitleKit"]$value
strMsgTitleKit <- ifelse(is.na(strtmp), strMsgTitleKit, 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)
})
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 = strFrmKits,
horizontal = TRUE,
spacing = 1,
container = gv,
expand = TRUE,
fill = TRUE
)
scroll_view <- ggroup(
horizontal = FALSE,
use.scrollwindow = TRUE,
container = f0,
expand = TRUE,
fill = TRUE
)
# Set initial minimal size.
size(scroll_view) <- c(100, 150)
kit_checkbox_group <- gcheckboxgroup(
items = getKit(),
checked = FALSE,
horizontal = FALSE,
container = scroll_view
)
addHandlerChanged(kit_checkbox_group, handler = function(h, ...) {
val_kits <- svalue(kit_checkbox_group)
if (debug) {
print("val_kits")
print(val_kits)
}
# check if any selected kit.
if (length(val_kits) > 0) {
# Enable analyse button.
enabled(analyse_btn) <- TRUE
# Suggest a save name.
svalue(save_edt) <- paste(paste(val_kits, collapse = "_"),
"_OL",
sep = ""
)
} else {
# Disable analyse button.
enabled(analyse_btn) <- FALSE
# Empty save name.
svalue(save_edt) <- ""
}
})
# FRAME 1 ###################################################################
f1 <- gframe(
text = strFrmOptions,
horizontal = FALSE,
spacing = 1,
container = gv
)
glabel(
text = strLblDatabase,
anchor = c(-1, 0), container = f1
)
f1_db_names <- getDb()
f1_db_drp <- gcombobox(
items = f1_db_names, fill = FALSE,
selected = 1, container = f1, ellipsize = "none"
)
f1_virtual_chk <- gcheckbox(
text = strChkVirtual,
checked = TRUE,
container = f1
)
tooltip(f1_virtual_chk) <- strTipVirtual
f1_limit_chk <- gcheckbox(
text = strChkLowFreq,
checked = TRUE,
container = f1
)
# 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 ####################################################################
analyse_btn <- gbutton(text = strBtnCalculate, container = gv)
addHandlerClicked(analyse_btn, handler = function(h, ...) {
val_name <- svalue(save_edt)
val_kits <- svalue(kit_checkbox_group)
val_kitData <- data.frame() # Filled further down.
val_db_selected <- svalue(f1_db_drp)
val_db <- NULL # Filled further down.
val_virtual <- svalue(f1_virtual_chk)
val_limit <- svalue(f1_limit_chk)
if (length(val_kits) > 0) {
# Change button.
blockHandlers(analyse_btn)
svalue(analyse_btn) <- strBtnProcessing
unblockHandlers(analyse_btn)
enabled(analyse_btn) <- FALSE
# Get kits.
for (k in seq(along = val_kits)) {
tmp <- getKit(val_kits[k])
val_kitData <- rbind(val_kitData, tmp)
}
# Get allele frequency database.
val_db <- getDb(val_db_selected)
if (debug) {
print("val_kits")
print(val_kits)
print("val_virtual")
print(val_virtual)
print("val_limit")
print(val_limit)
}
# Analyse bins overlap.
datanew <- calculateOL(
kit = val_kitData,
db = val_db,
virtual = val_virtual,
limit = val_limit,
debug = debug
)
# Create key-value pairs to log.
keys <- list("kit", "db", "virtual", "limit")
values <- list(val_kits, val_db_selected, val_virtual, val_limit)
# 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(str(datanew))
print(paste("EXIT:", fnc))
}
# Close GUI.
.saveSettings()
dispose(w)
} else {
gmessage(
mmsg = strMsgKit,
title = strMsgTitleKit,
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_calculateOL_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateOL_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_calculateOL_gui_db_name", envir = env, inherits = FALSE)) {
svalue(f1_db_drp) <- get(".strvalidator_calculateOL_gui_db_name", envir = env)
}
if (exists(".strvalidator_calculateOL_gui_virtual", envir = env, inherits = FALSE)) {
svalue(f1_virtual_chk) <- get(".strvalidator_calculateOL_gui_virtual", envir = env)
}
if (exists(".strvalidator_calculateOL_gui_limit", envir = env, inherits = FALSE)) {
svalue(f1_limit_chk) <- get(".strvalidator_calculateOL_gui_limit", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateOL_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateOL_gui_db_name", value = svalue(f1_db_drp), envir = env)
assign(x = ".strvalidator_calculateOL_gui_virtual", value = svalue(f1_virtual_chk), envir = env)
assign(x = ".strvalidator_calculateOL_gui_limit", value = svalue(f1_limit_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateOL_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateOL_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateOL_gui_db_name", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateOL_gui_db_name", envir = env)
}
if (exists(".strvalidator_calculateOL_gui_virtual", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateOL_gui_virtual", envir = env)
}
if (exists(".strvalidator_calculateOL_gui_limit", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateOL_gui_limit", 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)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.