Nothing
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# CHANGE LOG (last 20 changes)
# 05.09.2022: Compacted gui. Fixed narrow dropdowns. Removed destroy workaround.
# 03.03.2020: Fixed reference to function name.
# 01.03.2020: Added language support.
# 03.03.2019: Compacted and tweaked widgets under tcltk.
# 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'.
# 15.08.2016: Added save settings.
# 14.08.2016: Renamed to calculateCopies_gui and implementing new calculateCopies.
# 16.06.2016: 'Save as' textbox expandable.
# 28.08.2015: Added importFrom
# 11.10.2014: Added 'focus', added 'parent' parameter.
# 28.06.2014: Added help button and moved save gui checkbox.
# 08.05.2014: Implemented 'checkDataset'.
# 18.07.2013: Check before overwrite object.
# 11.06.2013: Added 'inherits=FALSE' to 'exists'.
# 04.06.2013: Fixed bug in 'missingCol'.
# 24.05.2013: Improved error message for missing columns.
#' @title Calculate Allele Copies
#'
#' @description
#' GUI wrapper for the \code{link{calculateCopies}} function.
#'
#' @details
#' Simplifies the use of the \code{\link{calculateCopies}} function by
#' providing a graphical user interface to it.
#'
#' @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
#'
#' @seealso \code{\link{calculateCopies}}
calculateCopies_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 allele copies"
strChkGui <- "Save GUI settings"
strBtnHelp <- "Help"
strFrmDataset <- "Dataset"
strLblDataset <- "Sample dataset:"
strDrpDefault <- "<Select dataset>"
strLblSamples <- "samples"
strFrmOptions <- "Options"
strChkObserved <- "Add number of unique alleles (count number of peaks)"
strChkCopies <- "Add number of allele copies (for known complete profiles)"
strTipCopies <- "'1' for heterozygotes and '2' for homozygotes."
strChkHeterozygosity <- "Add heterozygote indicator (for known complete profiles)"
strTipHeterozygosity <- "'1' for heterozygous loci and '0' for homozygous loci."
strFrmSave <- "Save as"
strLblSave <- "Name for result:"
strBtnCalculate <- "Calculate"
strBtnProcessing <- "Processing..."
strMsgDataset <- "A dataset has to 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"]$value
strLblDataset <- ifelse(is.na(strtmp), strLblDataset, strtmp)
strtmp <- dtStrings["strDrpDefault"]$value
strDrpDefault <- ifelse(is.na(strtmp), strDrpDefault, strtmp)
strtmp <- dtStrings["strLblSamples"]$value
strLblSamples <- ifelse(is.na(strtmp), strLblSamples, strtmp)
strtmp <- dtStrings["strFrmOptions"]$value
strFrmOptions <- ifelse(is.na(strtmp), strFrmOptions, strtmp)
strtmp <- dtStrings["strChkObserved"]$value
strChkObserved <- ifelse(is.na(strtmp), strChkObserved, strtmp)
strtmp <- dtStrings["strChkCopies"]$value
strChkCopies <- ifelse(is.na(strtmp), strChkCopies, strtmp)
strtmp <- dtStrings["strTipCopies"]$value
strTipCopies <- ifelse(is.na(strtmp), strTipCopies, strtmp)
strtmp <- dtStrings["strChkHeterozygosity"]$value
strChkHeterozygosity <- ifelse(is.na(strtmp), strChkHeterozygosity, strtmp)
strtmp <- dtStrings["strTipHeterozygosity"]$value
strTipHeterozygosity <- ifelse(is.na(strtmp), strTipHeterozygosity, strtmp)
strtmp <- dtStrings["strFrmSave"]$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"]$value
strMsgTitleDataset <- ifelse(is.na(strtmp), strMsgTitleDataset, strtmp)
}
# ---------------------------------------------------------------------------
# Main window.
w <- gwindow(title = strWinTitle, visible = FALSE)
# Runs when window is closed.
addHandlerUnrealize(w, handler = function(h, ...) {
# Save GUI state.
.saveSettings()
# Focus on parent window.
if (!is.null(parent)) {
focus(parent)
}
# Destroys window.
return(FALSE)
})
# Vertical main group.
gv <- ggroup(
horizontal = FALSE,
spacing = 1,
use.scrollwindow = FALSE,
container = w,
expand = FALSE,
fill = "x"
)
# Help button group.
gh <- ggroup(container = gv, expand = FALSE, fill = "both")
savegui_chk <- gcheckbox(
text = strChkGui, checked = FALSE,
container = gh
)
enabled(savegui_chk) <- FALSE
addSpring(gh)
help_btn <- gbutton(text = strBtnHelp, container = gh)
addHandlerChanged(help_btn, handler = function(h, ...) {
# Open help page for function.
print(help(fnc, help_type = "html"))
})
# FRAME 0 ###################################################################
f0 <- gframe(
text = strFrmDataset, horizontal = TRUE, spacing = 1,
container = gv, expand = FALSE, fill = "x"
)
# Datasets ------------------------------------------------------------------
glabel(text = strLblDataset, container = f0)
samples_lbl <- glabel(text = paste(" 0", strLblSamples), container = f0)
dataset_drp <- gcombobox(
items = c(
strDrpDefault,
listObjects(
env = env,
obj.class = "data.frame"
)
),
selected = 1, editable = FALSE, container = f0,
ellipsize = "none",
expand = TRUE,
fill = "x"
)
addHandlerChanged(dataset_drp, handler = function(h, ...) {
val_obj <- svalue(dataset_drp)
# Check if suitable.
requiredCol <- c("Sample.Name", "Marker", "Allele")
ok <- checkDataset(
name = val_obj, reqcol = requiredCol,
env = env, parent = w, debug = debug
)
if (ok) {
# Load or change components.
.gData <<- get(val_obj, envir = env)
.gDataName <<- val_obj
samples <- length(unique(.gData$Sample.Name))
svalue(samples_lbl) <- paste(" ", samples, strLblSamples)
svalue(save_edt) <- paste(val_obj, "_cop", sep = "")
} 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
)
f1_observed_chk <- gcheckbox(
text = strChkObserved,
checked = FALSE, container = f1
)
f1_copies_chk <- gcheckbox(
text = strChkCopies,
checked = TRUE, container = f1
)
tooltip(f1_copies_chk) <- strTipCopies
f1_het_chk <- gcheckbox(
text = strChkHeterozygosity,
checked = FALSE, container = f1
)
tooltip(f1_het_chk) <- strTipHeterozygosity
# 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_name <- svalue(save_edt)
val_data <- .gData
val_data_name <- .gDataName
val_obs <- svalue(f1_observed_chk)
val_cop <- svalue(f1_copies_chk)
val_het <- svalue(f1_het_chk)
if (!is.null(val_data)) {
# Change button.
blockHandlers(calculate_btn)
svalue(calculate_btn) <- strBtnProcessing
unblockHandlers(calculate_btn)
enabled(calculate_btn) <- FALSE
datanew <- calculateCopies(
data = val_data, observed = val_obs,
copies = val_cop, heterozygous = val_het,
debug = debug
)
# Create key-value pairs to log.
keys <- list("data", "observed", "copies", "heterozygous")
values <- list(val_data_name, val_obs, val_cop, val_het)
# 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(datanew)
print(paste("EXIT:", fnc))
}
# Close GUI.
.saveSettings()
dispose(w)
} else {
gmessage(
msg = strMsgDataset, title = strMsgTitleDataset,
icon = "error", parent = w
)
}
})
.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_calculateCopies_gui_savegui", envir = env, inherits = FALSE)) {
svalue(savegui_chk) <- get(".strvalidator_calculateCopies_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_calculateCopies_gui_observed", envir = env, inherits = FALSE)) {
svalue(f1_observed_chk) <- get(".strvalidator_calculateCopies_gui_observed", envir = env)
}
if (exists(".strvalidator_calculateCopies_gui_copies", envir = env, inherits = FALSE)) {
svalue(f1_copies_chk) <- get(".strvalidator_calculateCopies_gui_copies", envir = env)
}
if (exists(".strvalidator_calculateCopies_gui_het", envir = env, inherits = FALSE)) {
svalue(f1_het_chk) <- get(".strvalidator_calculateCopies_gui_het", envir = env)
}
if (debug) {
print("Saved settings loaded!")
}
}
}
.saveSettings <- function() {
# Then save settings if true.
if (svalue(savegui_chk)) {
assign(x = ".strvalidator_calculateCopies_gui_savegui", value = svalue(savegui_chk), envir = env)
assign(x = ".strvalidator_calculateCopies_gui_observed", value = svalue(f1_observed_chk), envir = env)
assign(x = ".strvalidator_calculateCopies_gui_copies", value = svalue(f1_copies_chk), envir = env)
assign(x = ".strvalidator_calculateCopies_gui_het", value = svalue(f1_het_chk), envir = env)
} else { # or remove all saved values if false.
if (exists(".strvalidator_calculateCopies_gui_savegui", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateCopies_gui_savegui", envir = env)
}
if (exists(".strvalidator_calculateCopies_gui_observed", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateCopies_gui_observed", envir = env)
}
if (exists(".strvalidator_calculateCopies_gui_copies", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateCopies_gui_copies", envir = env)
}
if (exists(".strvalidator_calculateCopies_gui_het", envir = env, inherits = FALSE)) {
remove(".strvalidator_calculateCopies_gui_het", 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)
}
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