path: root/inst/GUI/gmkin.R

# gWidgetsWWW2 GUI for mkin {{{1

# Copyright (C) 2013,2014,2015 Johannes Ranke
# Portions of this file are copyright (C) 2013 Eurofins Regulatory AG, Switzerland
# Contact: jranke@uni-bremen.de

# This file is part of the R package gmkin

# gmkin is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.

# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
# details.

# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>

# Configuration {{{1
left_width = 250
right_width = 500
save_keybinding = "Ctrl-X"
gcb_observed_width = 100
gcb_type_width = 70
gcb_to_width = 160 
gcb_sink_width = 70

# Set the GUI title and create the basic widget layout {{{1
# Three panel layout {{{2
window_title <- paste0("gmkin ", packageVersion("gmkin"),
                       "- Browser based GUI for kinetic evaluations using mkin")
w  <- gwindow(window_title)
sb <- gstatusbar(paste("Powered by gWidgetsWWW2 (ExtJS, Rook)",
                       "and mkin (FME, deSolve and minpack.lm)",
                       "--- Working directory is", getwd()), cont = w)

bl <- gborderlayout(cont = w,
                    #title = list(center = "Work", east = "Results"),
                    panels = c("center", "west", "east"),
                    collapsible = list(west = FALSE))

bl$set_panel_size("west", left_width)
bl$set_panel_size("east", right_width)

center <- gnotebook(cont = bl, where = "center")
left   <- gvbox(cont = bl, use.scrollwindow = TRUE, where = "west")
right   <- gnotebook(cont = bl, use.scrollwindow = TRUE, where = "east")

# Helper functions {{{1
# Override function for making it possible to override original data points using the GUI {{{2
override <- function(d) {
  if (!is.null(d$override)) {
    d_new <- data.frame(name = d$name, time = d$time, 
                        value = ifelse(is.na(d$override), d$value, d$override),
                        err = d$err)
    return(d_new)
  } else {
    return(d)
  }
}
# Update dataframe with projects {{{2
update_p.df <- function() {
  wd_projects <- gsub(".gmkinws", "", dir(pattern = ".gmkinws$"))
  if (length(wd_projects) > 0) {
    p.df.wd <- data.frame(Name = wd_projects, 
                          Source = rep("working directory",
                                       length(wd_projects)),
                          stringsAsFactors = FALSE)
    p.df <<- rbind(p.df.package, p.df.wd)
  } else {
    p.df <<- p.df.package
  }
  p.gtable[,] <- p.df
  p.line.import.p[,] <- c("", p.df$Name)
}
# Update dataframe with datasets {{{2
update_ds.df <- function() {
  if (is.na(ws$ds[1])) ds.df <<- ds.df.empty
  else ds.df <<- data.frame(Title = sapply(ws$ds, function(x) x$title), stringsAsFactors = FALSE)
  ds.gtable[,] <- ds.df
  update_ds_editor()
  ds.delete$call_Ext("disable")  
  ds.copy$call_Ext("disable")  
}
# Update dataframe with models {{{2
update_m.df <- function() {
  if (is.na(ws$m[1])) m.df <<- m.df.empty
  else m.df <<- data.frame(Name = sapply(ws$m, function(x) x$name), stringsAsFactors = FALSE)
  m.gtable[,] <- m.df
  update_m_editor()
  m.delete$call_Ext("disable")  
  m.copy$call_Ext("disable")  
}
# Update dataframe with fits {{{2
update_f.df <- function() {
  f.df <- f.df.empty
  if (!is.na(ftmp[1])) {
    f.df[1, "Name"] <- c("Temporary (not fitted)")
  }
  if (!is.na(ws$f[1])) {
    f.df.ws <- data.frame(Name = sapply(ws$f, function(x) x$name),
                          stringsAsFactors = FALSE)
    f.df <- rbind(f.df, f.df.ws)
  }
  f.df <<- f.df
}
# Generate the initial workspace {{{1
# Project workspace {{{2
ws <- gmkinws$new()
ws.import <- NA
# Initialise meta data objects so assignments within functions using <<- will {{{2
# update them in the right environment.
# Also create initial versions of meta data in order to be able to clear the workspace
p.df <- p.df.package <- data.frame(Name = c("FOCUS_2006", "FOCUS_2006_Z"),
                                   Source = rep("gmkin package", 2), stringsAsFactors = FALSE)
# Datasets {{{2
ds.empty <- mkinds$new(
  title = "New dataset", time_unit = "", unit = "",
  data = data.frame(
    name = rep(c("parent", "m1"), each = 5),
    time = rep(c(0, 1, 4, 7, 14), 2),
    value = c(100, rep(NA, 9)),
    override = "NA", err = 1,
    stringsAsFactors = FALSE))
ds.cur <- ds.empty$clone()
ds.df <- ds.df.empty <- data.frame(Title = "", stringsAsFactors = FALSE)
# Models {{{2
m.empty <- mkinmod(parent = mkinsub("SFO"))
m.empty$name <- ""
m.empty$spec <- list()
m.cur <- m.empty
m.df <- m.df.empty <- data.frame(Name = "", stringsAsFactors = FALSE)
# Fits {{{2
f.df <- f.df.empty <- data.frame(Name = "", stringsAsFactors = FALSE)
ftmp <- NA
# left: Explorer tables {{{1
# Frames {{{2
p.gf  <- gframe("Projects", cont = left, horizontal = FALSE)
ds.gf <- gframe("Datasets", cont = left)
m.gf <-  gframe("Models", cont = left)
c.gf <-  gframe("Configuration", cont = left, horizontal = FALSE)
f.gf <-  gframe("Results", cont = left)

# Project explorer {{{2
# Initialize project list from the gmkin package and the current working directory
# The former must be manually amended if additional workspaces should be available
p.gtable <- gtable(p.df, cont = p.gf, width = left_width - 10, height = 120)
size(p.gtable) <- list(columnWidths = c(130, 100))
p.loaded <- NA # The index of the loaded project. We reset the selection to this when the user 
               # does not confirm
p.modified <- FALSE # Keep track of modifications after loading
p.switcher <- function(h, ...) {
  p.cur <- h$row_index # h$row_index for clicked or doubleclick handlers, h$value for change
  project_switched <- FALSE
  switch_project <- function() {
    Name <- p.df[p.cur, "Name"]
    if (p.df[p.cur, "Source"] == "working directory") {
      load(paste0(Name, ".gmkinws"))
      ws <<- ws
    } else {
      ws <<-  get(Name)$clone()
    }
    svalue(center) <- 1
    svalue(c.ds) <- empty_conf_labels[1]
    svalue(c.m) <- empty_conf_labels[2]
    update_p_editor(p.cur)
    update_ds.df()
    update_m.df()
    m.gtable[,] <<- m.df
    update_f.df()
    f.gtable[,] <<- f.df
    p.loaded <<- p.cur
    project_switched <- TRUE
    p.gtable$set_index(p.cur)
    p.modified <<- FALSE
  }
  if (p.modified) {
    gconfirm("When you switch projects, you loose any unsaved changes. Proceed to switch?",
             handler = function(h, ...) { 
      switch_project()
    })
  } else {
    switch_project()
  }
  # We can reset the selection only if the project was not
  # switched. The following code gets executed during the confirmation dialogue,
  # i.e. before the potential switching
  if (!project_switched) {
    if (is.na(p.loaded)) {
      p.gtable$clear_selection()
    } else {
      p.gtable$set_index(p.loaded)
    }
  }
}
addHandlerClicked(p.gtable, p.switcher)
# Dataset explorer {{{2
ds.switcher <- function(h, ...) {
  ds.i <- h$row_index
  svalue(c.ds) <- ds.df[ds.i, "Title"]
  ds.cur <<- ws$ds[[ds.i]]
  update_ds_editor()
  ds.delete$call_Ext("enable")  
  ds.copy$call_Ext("enable")  
  if (!is.na(svalue(m.gtable))) c.conf$call_Ext("enable")
  svalue(center) <- 2
  svalue(right) <- 2
}
ds.gtable <- gtable(ds.df, cont = ds.gf, width = left_width - 10, height = 160)
addHandlerClicked(ds.gtable, ds.switcher)
# Model explorer {{{2
m.switcher <- function(h, ...) {
  m.i <- h$row_index
  svalue(c.m) <- m.df[m.i, "Name"]
  m.cur <<- ws$m[[m.i]] 
  update_m_editor()
  m.delete$call_Ext("enable")  
  m.copy$call_Ext("enable")  
  if (!is.na(svalue(ds.gtable))) c.conf$call_Ext("enable")
  svalue(center) <- 3
  svalue(right) <- 3
}
m.gtable <- gtable(m.df, cont = m.gf, width = left_width - 10, height = 160)
addHandlerClicked(m.gtable, m.switcher)
# Fit explorer {{{2
f.switcher <- function(h, ...) {
  f.cur <<- h$row_index - 1
  if (f.cur > 0) {
    ftmp <<- ws$f[[f.cur]]
    c.ds$call_Ext("setText", 
       paste0("<font color='gray'>", ftmp$ds$title, "</font>"), FALSE)
    c.m$call_Ext("setText", 
       paste0("<font color='gray'>", ftmp$mkinmod$name, "</font>"), FALSE)
    c.conf$call_Ext("disable")
  }
  ds.gtable$clear_selection()
  m.gtable$clear_selection()
  #update_f_conf()
  #update_f_results()
  svalue(center) <- 5
}
f.gtable <- gtable(f.df, cont = f.gf, width = left_width - 10, height = 160)
addHandlerClicked(f.gtable, f.switcher)
# Configuration {{{2
configure_fit_handler <- function(h, ...) {

  svalue(center) <- 4
}

empty_conf_labels <- paste0("<font color='gray'>Current ", c("dataset", "model"), "</font>")
c.ds <- glabel(empty_conf_labels[1], cont = c.gf)
c.m <- glabel(empty_conf_labels[2], cont = c.gf)
c.conf <- gbutton("Configure fit", cont = c.gf, handler = configure_fit_handler,
                  ext.args = list(disabled = TRUE))
# center: Project editor {{{1
p.editor  <- gframe("", horizontal = FALSE, cont = center, 
                     label = "Project")
# Line with buttons {{{2
p.line.buttons <- ggroup(cont = p.editor, horizontal = TRUE)
p.new <- gbutton("New project", cont = p.line.buttons,
  handler = function(h, ...) {
    project_name <- "New project"
    svalue(p.name) <- project_name
    svalue(p.filename) <- file.path(getwd(), paste0(project_name, ".gmkinws"))
    svalue(p.observed) <- ""
    p.delete$call_Ext("disable")
    ws <<- gmkinws$new()
    update_ds.df()
    update_m.df()
    m.gtable[,] <- m.df
    update_f.df()
    f.gtable[,] <- f.df
  })
p.delete.handler = function(h, ...) {
  filename <- file.path(getwd(), paste0(svalue(p.name), ".gmkinws"))
  gconfirm(paste0("Are you sure you want to delete ", filename, "?"),
           parent = w,
           handler = function(h, ...) {
             if (inherits(try(unlink(filename)), "try-error")) {
               gmessage("Deleting failed for an unknown reason", cont = w)
             } else {
               svalue(sb) <- paste("Deleted", filename)
               svalue(p.filename) <- ""
               svalue(p.observed) <- ""
               p.delete$call_Ext("disable")
               update_p.df()
             }
           })
}
p.delete <- gbutton("Delete project", cont = p.line.buttons,
                    handler = p.delete.handler,
                    ext.args = list(disabled = TRUE))
# Project name {{{2
p.line.name <- ggroup(cont = p.editor, horizontal = TRUE)
p.name  <- gedit("New project", label = "<b>Project name</b>",
                 width = 50, cont = p.line.name)
p.save.action <- gaction("Save", parent = w,
  handler = function(h, ...) {
    filename <- paste0(svalue(p.name), ".gmkinws")
    try_to_save <- function (filename) {
      if (!inherits(try(save(ws, file = filename)),
                    "try-error")) {
        svalue(sb) <- paste("Saved project to file", filename,
                            "in working directory", getwd())
        update_p.df()
        p.modified <<- FALSE
      } else {
        gmessage("Saving failed for an unknown reason", parent = w)
      }
    }
    if (file.exists(filename)) {
      gconfirm(paste("File", filename, "exists. Overwrite?"),
               parent = w, 
               handler = function(h, ...) {
        try_to_save(filename)
      })
    } else {
      try_to_save(filename)
    }
  })
p.save.action$add_keybinding(save_keybinding)
p.save <- gbutton(action = p.save.action, cont = p.line.name)
tooltip(p.save) <- paste("Press", save_keybinding, "to save")

update_p_editor <- function(p.cur) {
  project_name <-  as.character(p.df[p.cur, "Name"])
  svalue(p.name)  <- project_name
  if (p.df[p.cur, "Source"] == "gmkin package") {
    svalue(p.filename) <- ""
    p.delete$call_Ext("disable")
  } else {
    svalue(p.filename) <- file.path(getwd(), paste0(project_name, ".gmkinws"))
    p.delete$call_Ext("enable")
  }
  svalue(p.observed) <- paste(ws$observed, collapse = ", ")
}
# Working directory {{{2
p.line.wd <- ggroup(cont = p.editor, horizontal = TRUE)
wd_handler <- function(h, ...) {
 target_wd <- svalue(p.wde)
 wd <- try(setwd(target_wd))
 if (inherits(wd, "try-error")) {
   gmessage(paste("Could not set working directory to", target_wd), parent = w)
 } else {
   svalue(sb) <- paste("Changed working directory to", wd)
   update_p.df()
 }
}
p.wde <- gedit(getwd(), cont = p.line.wd, label = "Working directory", width = 50)
p.wde$add_handler_enter(wd_handler)
p.wdb <- gbutton("Change", cont = p.line.wd, handler = wd_handler)
tooltip(p.wdb) <- "Edit the box on the left and press enter to change"
# File name {{{2
p.line.file <- ggroup(cont = p.editor, horizontal = TRUE)
p.filename.gg  <- ggroup(width = 135, cont = p.line.file) # for spacing
p.filename.label <- glabel("Project file:", cont = p.filename.gg)
p.filename  <- glabel("", cont = p.line.file)
# Observed variables {{{2
p.line.observed <- ggroup(cont = p.editor, horizontal = TRUE)
p.observed.gg  <- ggroup(width = 135, cont = p.line.observed) # for spacing
p.observed.label <- glabel("Observed variables:", cont = p.observed.gg)
p.observed  <- glabel("", cont = p.line.observed)
# Import {{{2
p.line.import <- ggroup(cont = p.editor, horizontal = TRUE)
p.line.import.p <- gcombobox(c("", p.df$Name), label = "Import from", cont = p.line.import,
  handler = function(h, ...) {
    p.import <- svalue(h$obj, index = TRUE) - 1
    Name <- p.df[p.import, "Name"]
    if (p.df[p.import, "Source"] == "working directory") {
      load(paste0(Name, ".gmkinws"))
      ws.import <<- ws
    } else {
      ws.import <<- get(Name)
    }
    p.line.import.dst[,] <- data.frame(Title = sapply(ws.import$ds, function(x) x$title),
                                       stringsAsFactors = FALSE)
    p.line.import.mt[,] <- data.frame(Name = sapply(ws.import$m, function(x) x$name),
                                      stringsAsFactors = FALSE)
  })
p.line.import.frames <- ggroup(cont = p.editor, horizontal = TRUE)

p.line.import.dsf <- gframe("Datasets for import", cont = p.line.import.frames, horizontal = FALSE)
p.line.import.dst <- gtable(ds.df.empty, cont = p.line.import.dsf, multiple = TRUE,
                            width = left_width - 10, height = 160,
                            handler = function(h, ...) p.line.import.dsb$call_Ext("enable"))
p.line.import.dsb <- gbutton("Import selected", cont = p.line.import.dsf,
  ext.args = list(disabled = TRUE),
  handler = function(h, ...) {
    i <- svalue(p.line.import.dst, index = TRUE)
    ws$add_ds(ws.import$ds[i])
    update_ds.df()
    svalue(p.observed) <- paste(ws$observed, collapse = ", ")
    p.modified <<- TRUE
  }
)

p.line.import.mf <- gframe("Models for import", cont = p.line.import.frames, horizontal = FALSE)
p.line.import.mt <- gtable(m.df.empty, cont = p.line.import.mf, multiple = TRUE,
                            width = left_width - 10, height = 160,
                            handler = function(h, ...) p.line.import.mb$call_Ext("enable"))
p.line.import.mb <- gbutton("Import selected", cont = p.line.import.mf,
  ext.args = list(disabled = TRUE),
  handler = function(h, ...) {
    i <- svalue(p.line.import.mt, index = TRUE)
    ws$add_m(ws.import$m[i])
    update_m.df()
    m.gtable[,] <- m.df
    svalue(p.observed) <- paste(ws$observed, collapse = ", ")
    p.modified <<- TRUE
  }
)
# center: Dataset editor {{{1
ds.editor <- gframe("", horizontal = FALSE, cont = center, 
                     label = "Dataset")
# Handler functions {{{2
# For top row buttons {{{3
stage_dataset <- function(ds.new) {
  ds.cur <<- ds.new
  update_ds_editor()
  ds.copy$call_Ext("disable")
  ds.delete$call_Ext("disable")
}

add_dataset <- function(ds.new) {
  ws$add_ds(list(ds.new))
  update_ds.df()
  p.modified <<- TRUE
}

new_dataset_handler <- function(h, ...) {
  ds.new <- ds.empty$clone()
  ds.new$title <- "New dataset"
  stage_dataset(ds.new)
}

copy_dataset_handler <- function(h, ...) {
  ds.new <- ds.cur$clone()
  ds.new$title <- paste("Copy of ", ds.cur$title)
  stage_dataset(ds.new)
}
  
delete_dataset_handler <- function(h, ...) {
  ds.i <- svalue(ds.gtable, index = TRUE)
  ws$delete_ds(ds.i)
  update_ds.df()
  p.modified <<- TRUE
}

keep_ds_changes_handler <- function(h, ...) {
  add_dataset(
    mkinds$new(
      title = svalue(ds.title.ge),
      data = ds.e.gdf[,], 
      time_unit = svalue(ds.e.stu),
      unit = svalue(ds.e.obu)))
  update_ds.df()
  ds.gtable$set_index(length(ws$ds))
  update_ds_editor()
  svalue(p.observed) <- paste(ws$observed, collapse = ", ")
}

# For populating the dataset editor {{{3
empty_grid_handler <- function(h, ...) {
  obs <- strsplit(svalue(ds.e.obs), ", ")[[1]]
  sampling_times_to_parse <- paste0("c(", svalue(ds.e.st), ")")
  sampling_times <- eval(parse(text = sampling_times_to_parse))
  replicates <- as.numeric(svalue(ds.e.rep))
  new.data = data.frame(
    name = rep(obs, each = replicates * length(sampling_times)),
    time = as.numeric(rep(sampling_times, each = replicates, times = length(obs))),
    value = as.numeric(NA),
    override = as.numeric(NA),
    err = 1,
    stringsAsFactors = FALSE
  )
  ds.e.gdf[,] <- new.data
  svalue(right) <- 2
}

# For uploading {{{3
tmptextheader <- character(0)
load_text_file_with_data <- function(h, ...) {
  tmptextfile <<- normalizePath(svalue(h$obj), winslash = "/")
  tmptext <- readLines(tmptextfile, warn = FALSE)
  tmptextskip <<- 0
  for (tmptextline in tmptext) {
    if (grepl(":|#|/", tmptextline)) tmptextskip <<- tmptextskip + 1
    else break()
  }
  svalue(ds.e.up.skip) <- tmptextskip
  if (svalue(ds.e.up.header)) {
    tmptextheader <<- strsplit(tmptext[tmptextskip + 1], 
                             " |\t|;|,")[[1]]
  }
  svalue(ds.e.up.wide.time) <- tmptextheader[[1]]
  svalue(ds.e.up.long.time) <- tmptextheader[[2]]
  svalue(ds.e.up.text) <- c("<pre>", c(tmptext[1:5], "\n...\n"), "</pre>")
  visible(ds.e.import) <- TRUE
}
 
new_ds_from_csv_handler <- function(h, ...) {
   tmpd <- try(read.table(tmptextfile,
                          skip = as.numeric(svalue(ds.e.up.skip)), 
                          dec = svalue(ds.e.up.dec),
                          sep = switch(svalue(ds.e.up.sep), 
                                       whitespace = "", 
                                       ";" = ";",
                                       "," = ","),
                          header = svalue(ds.e.up.header),
                          stringsAsFactors = FALSE))
  if(svalue(ds.e.up.widelong) == "wide") {
    tmpdl <- mkin_wide_to_long(tmpd, time = as.character(svalue(ds.e.up.wide.time)))
  } else {
    tmpdl <- data.frame(
      name = tmpd[[svalue(ds.e.up.long.name)]],
      time = tmpd[[svalue(ds.e.up.long.time)]],
      value = tmpd[[svalue(ds.e.up.long.value)]])
    tmpderr <- tmpd[[svalue(ds.e.up.long.err)]]
    if (!is.null(tmpderr)) tmpdl$err <- tmpderr
  }
  if (class(tmpd) != "try-error") {
    ds.cur <<- mkinds$new(
      title = "New import",
      time_unit = "",
      unit = "",
      data = tmpdl)
    if (is.null(ds.cur$data$err)) ds.cur$data$err <<- 1
    update_ds.df()
    update_ds_editor()
  } else {
    galert("Uploading failed", parent = "w")
  }
}

# Update the dataset editor {{{3
update_ds_editor <- function() {
  svalue(ds.title.ge) <- ds.cur$title
  svalue(ds.e.st) <- paste(ds.cur$sampling_times, collapse = ", ")
  svalue(ds.e.stu) <- ds.cur$time_unit
  svalue(ds.e.obs) <- paste(ds.cur$observed, collapse = ", ")
  svalue(ds.e.obu) <- ds.cur$unit
  svalue(ds.e.rep) <- ds.cur$replicates
  ds.e.gdf[,] <- ds.cur$data
  ds.keep$call_Ext("enable")
  visible(ds.e.import) <- FALSE
  svalue(ds.e.up.text) <- "<pre></pre>"
}
# Widget setup {{{2
# Line 1 with buttons {{{3
ds.e.buttons <- ggroup(cont = ds.editor, horizontal = TRUE)
ds.e.new <- gbutton("New dataset", cont = ds.e.buttons, handler = new_dataset_handler)
ds.copy <- gbutton("Copy dataset", cont = ds.e.buttons,
  handler = copy_dataset_handler, ext.args = list(disabled = TRUE))
ds.delete <- gbutton("Delete dataset", cont = ds.e.buttons, 
  handler = delete_dataset_handler, ext.args = list(disabled = TRUE))
ds.keep <- gbutton("Keep changes", cont = ds.e.buttons, handler = keep_ds_changes_handler)
ds.keep$call_Ext("disable")

# Formlayout for meta data {{{3
ds.e.gfl <- gformlayout(cont = ds.editor)
ds.title.ge <- gedit(label = "<b>Dataset title</b>", width = 60, cont = ds.e.gfl)
ds.e.st     <- gedit(width = 60, label = "Sampling times", cont = ds.e.gfl)
ds.e.stu    <- gedit(width = 20, label = "Unit", cont = ds.e.gfl)
ds.e.rep    <- gedit(width = 20, label = "Replicates", cont = ds.e.gfl)
ds.e.obs    <- gedit(width = 60, label = "Observed", cont = ds.e.gfl)
ds.e.obu    <- gedit(width = 20, label = "Unit", cont = ds.e.gfl)
generate_grid.gb <- gbutton("Generate grid for entering kinetic data", cont = ds.editor, 
        handler = empty_grid_handler)
tooltip(generate_grid.gb) <- "Overwrites the kinetic data shown to the right"

# Data upload area {{{3
tmptextfile <- "" # Initialize file name for imported data
tmptextskip <- 0 # Initialize number of lines to be skipped
tmptexttime <- "V1" # Initialize name of time variable if no header row
upload_dataset.gf <- gfile(text = "Upload text file", cont = ds.editor,
        handler = load_text_file_with_data)


# Import options {{{3
ds.e.import <- ggroup(cont = ds.editor, horizontal = FALSE)
visible(ds.e.import) <- FALSE
ds.e.preview <- ggroup(cont = ds.e.import, width = 480,  height = 150,
                      ext.args = list(layout = list(type="vbox", align = "center")))
ds.e.up.text <- ghtml("<pre></pre>", cont = ds.e.preview, width = 400, height = 150)
ds.e.up.import <- gbutton("Import using options specified below", cont = ds.e.import,
                          handler = new_ds_from_csv_handler)
ds.e.up.options <- ggroup(cont = ds.e.import, width = 200, horizontal = FALSE)
ds.e.up.skip <- gedit(tmptextskip, label = "Comment lines", width = 20, cont = ds.e.up.options)
ds.e.up.header <- gcheckbox(cont = ds.e.up.options, label = "Column names",
                            checked = TRUE)
ds.e.up.sep <- gcombobox(c("whitespace", ";", ","), cont = ds.e.up.options, width = 50,
                         selected = 1, label = "Separator")
ds.e.up.dec <- gcombobox(c(".", ","), cont = ds.e.up.options, width = 100,
                         selected = 1, label = "Decimal")
ds.e.up.widelong <- gradio(c("wide", "long"), horizontal = TRUE, width = 100,
                           label = "Format", cont = ds.e.up.options,
                           handler = function(h, ...) {
                             widelong = svalue(h$obj, index = TRUE)
                             svalue(ds.e.up.wlstack) <- widelong
                           })
ds.e.up.wlstack <- gstackwidget(cont = ds.e.import)
ds.e.up.wide <- ggroup(cont = ds.e.up.wlstack, horizontal = FALSE, width = 300)
ds.e.up.wide.time <- gedit(tmptexttime, cont = ds.e.up.wide, label = "Time column")
ds.e.up.long <- ggroup(cont = ds.e.up.wlstack, horizontal = FALSE, width = 300)
ds.e.up.long.name <- gedit("name", cont = ds.e.up.long, label = "Observed variables")
ds.e.up.long.time <- gedit(tmptexttime, cont = ds.e.up.long, label = "Time column")
ds.e.up.long.value <- gedit("value", cont = ds.e.up.long, label = "Value column")
ds.e.up.long.err <- gedit("err", cont = ds.e.up.long, label = "Relative errors")
svalue(ds.e.up.wlstack) <- 1

# center: Model editor {{{1
m.editor  <- gframe("", horizontal = FALSE, cont = center, 
                    label = "Model")
# Handler functions {{{2
# For top row buttons {{{3
stage_model <- function(m.new) {
  m.cur <<- m.new
  update_m_editor()
  m.copy$call_Ext("disable")
  m.delete$call_Ext("disable")
}

add_model <- function(m.new) {
  ws$add_m(list(m.new))
  update_m.df()
  p.modified <<- TRUE
}

new_model_handler <- function(h, ...) {
  m.new <- m.empty
  m.new$name <- "New model"
  stage_model(m.new)
}

copy_model_handler <- function(h, ...) {
  m.new <- m.cur
  m.new$name <- paste("Copy of ", m.cur$title)
  stage_model(m.new)
}
  
delete_model_handler <- function(h, ...) {
  m.i <- svalue(m.gtable, index = TRUE)
  ws$delete_m(m.i)
  update_m.df()
  p.modified <<- TRUE
}

keep_m_changes_handler <- function(h, ...) {
  spec <- list()
  for (obs.i in 1:length(m.e.rows)) {
    to_string <- svalue(m.e.to[[obs.i]])
    if (length(to_string) == 0) to_vector = NULL
    else to_vector = strsplit(svalue(m.e.to[[obs.i]]), ", ")[[1]]
    spec[[obs.i]] <- mkinsub(svalue(m.e.type[[obs.i]]),
                          to = to_vector,
                          sink = svalue(m.e.sink[[obs.i]]))
    names(spec)[[obs.i]] <- svalue(m.e.obs[[obs.i]])
  }
  m.cur <<- mkinmod(use_of_ff = svalue(m.ff.gc), 
                    speclist = spec)
  m.cur$name <<- svalue(m.name.ge) 
  add_model(m.cur)
  svalue(p.observed) <- paste(ws$observed, collapse = ", ")
}
# Add and remove observed variables {{{3
add_observed <- function(obs.i) {
  if (obs.i == length(ws$observed)) {
    m.add_observed$call_Ext("disable")
  }
  m.e.rows[[obs.i]] <<- ggroup(cont = m.editor, horizontal = TRUE)
  m.e.obs[[obs.i]] <<- gcombobox(ws$observed, 
                                 selected = obs.i, 
                                 width = gcb_observed_width,
                                 cont = m.e.rows[[obs.i]])
  obs.types <- if (obs.i == 1) c("SFO", "FOMC", "DFOP", "HS", "SFORB")
    else c("SFO", "SFORB")
  m.e.type[[obs.i]] <<- gcombobox(obs.types, width = gcb_type_width,
                                  selected = 0L, cont = m.e.rows[[obs.i]])
  glabel("to", cont = m.e.rows[[obs.i]]) 
  m.e.to[[obs.i]] <<- gcombobox(ws$observed, selected = 0L,
                                width = gcb_to_width,
                                ext.args = list(multiSelect = TRUE),
                                cont = m.e.rows[[obs.i]])
  m.e.sink[[obs.i]] <<- gcheckbox("Sink", width = gcb_sink_width,
                                  checked = TRUE, cont = m.e.rows[[obs.i]]) 
  if (obs.i > 1) {
    gbutton("Remove observed variable", handler = remove_observed_handler, 
            action = obs.i, cont = m.e.rows[[obs.i]])
  }
}

add_observed_handler <- function(h, ...) {
  obs.i <- length(m.e.rows) + 1
  add_observed(obs.i)
}

remove_observed_handler <- function(h, ...) {
  m.cur$spec[[h$action]] <<- NULL
  update_m_editor()
}
# Update the model editor {{{3
update_m_editor <- function() {
  svalue(m.name.ge) <- m.cur$name
  svalue(m.ff.gc) <- m.cur$use_of_ff
  for (oldrow.i in seq_along(m.e.rows)) {
    delete(m.editor, m.e.rows[[oldrow.i]])
  }
  m.keep$call_Ext("enable")
  m.e.rows <<- m.e.obs <<- m.e.type <<- m.e.to <<- m.e.sink <<- list()
  if (length(m.cur$spec) == length(ws$observed)) {
    m.add_observed$call_Ext("disable")
  } else {
    m.add_observed$call_Ext("enable")
  }
  show_m_spec()
}
# Widget setup {{{2
# Line 1 with buttons {{{3
m.e.buttons <- ggroup(cont = m.editor, horizontal = TRUE)
m.e.new <- gbutton("New model", cont = m.e.buttons, handler = new_model_handler)
m.copy <- gbutton("Copy model", cont = m.e.buttons,
  handler = copy_model_handler, ext.args = list(disabled = TRUE))
m.delete <- gbutton("Delete model", cont = m.e.buttons, 
  handler = delete_model_handler, ext.args = list(disabled = TRUE))
m.keep <- gbutton("Keep changes", cont = m.e.buttons, handler = keep_m_changes_handler)
m.keep$call_Ext("disable")

# Formlayout for meta data {{{3
m.e.gfl <- gformlayout(cont = m.editor)
m.name.ge <- gedit(label = "<b>Model name</b>", width = 60, cont = m.e.gfl)
m.ff.gc <- gcombobox(c("min", "max"), label = "Use of formation fractions", 
                     cont = m.e.gfl)
svalue(m.ff.gc) <- m.cur$use_of_ff
m.add_observed <- gbutton("Add observed variable", cont = m.editor,
  handler = add_observed_handler)
m.add_observed$call_Ext("disable")


# Model specification {{{3
m.e.rows <- m.e.obs <- m.e.type <- m.e.to <- m.e.sink <- list()

# Show the model specification {{{4
show_m_spec <- function() {
  for (obs.i in seq_along(m.cur$spec)) {
    obs.name <- names(m.cur$spec)[[obs.i]]

    add_observed(obs.i)

    svalue(m.e.obs[[obs.i]]) <<- obs.name
    svalue(m.e.type[[obs.i]]) <<- m.cur$spec[[obs.i]]$type
    obs.to = m.cur$spec[[obs.i]]$to
    obs.to_string_R = paste(obs.to, collapse = ", ")
    obs.to_string_JS = paste0("['", paste(obs.to, collapse = "', '"), "']")
    # Set R and Ext values separately, as multiple selections are not supported
    svalue(m.e.to[[obs.i]]) <<- obs.to_string_R
    m.e.to[[obs.i]]$call_Ext("select", String(obs.to_string_JS))
  }
}
show_m_spec()


# center: Fit configuration {{{1
f.config  <- gframe("", horizontal = FALSE, cont = center, 
                    label = "Configuration")
# Handler functions {{{2
run_fit <- function() { #{{{3
#   Parameters <- f.gg.parms[,]
#   Parameters.de <- subset(Parameters, Type == "deparm")
#   deparms <- Parameters.de$Initial
#   names(deparms) <- Parameters.de$Name
#   defixed <- names(deparms[Parameters.de$Fixed])
#   Parameters.ini <- subset(Parameters, Type == "state")
#   iniparms <- Parameters.ini$Initial
#   names(iniparms) <- sub("_0", "", Parameters.ini$Name)
#   inifixed <- names(iniparms[Parameters.ini$Fixed])
#   weight <- svalue(f.gg.opts.weight)
#   if (weight == "manual") {
#     err = "err"
#   } else {
#     err = NULL
#   }
#   reweight.method <- svalue(f.gg.opts.reweight.method)
#   if (reweight.method == "none") reweight.method = NULL
#   ftmp <<- mkinfit(ftmp$mkinmod, override(ds[[ds.i]]$data),
#                    state.ini = iniparms,
#                    fixed_initials = inifixed,
#                    parms.ini = deparms, 
#                    fixed_parms = defixed,
#                    plot = svalue(f.gg.opts.plot),
#                    solution_type = svalue(f.gg.opts.st),
#                    atol = as.numeric(svalue(f.gg.opts.atol)),
#                    rtol = as.numeric(svalue(f.gg.opts.rtol)),
#                    transform_rates = svalue(f.gg.opts.transform_rates),
#                    transform_fractions = svalue(f.gg.opts.transform_fractions),
#                    weight = weight,
#                    err = err,
#                    reweight.method = reweight.method,
#                    reweight.tol = as.numeric(svalue(f.gg.opts.reweight.tol)),
#                    reweight.max.iter = as.numeric(svalue(f.gg.opts.reweight.max.iter)),
#                    method.modFit = svalue(f.gg.opts.method.modFit),
#                    maxit.modFit = svalue(f.gg.opts.maxit.modFit)
#                    )
#   ftmp$ds.index <<- ds.i
#   ftmp$ds <<- ds[[ds.i]]
#   stmp <<- summary(ftmp)
#   show_plot("Optimised")
#   svalue(f.gg.opts.st) <- ftmp$solution_type
#   svalue(f.gg.opts.weight) <- ftmp$weight.ini
#   f.gg.parms[,] <- get_Parameters(stmp, TRUE)
#   svalue(f.gg.summary.filename) <<- paste(ftmp$ds$title, "_", ftmp$mkinmod$name, ".txt", sep = "")
#   svalue(f.gg.summary.listing) <<- c("<pre>", capture.output(stmp), "</pre>")
}
delete_fit_handler <- function(h, ...) { # {{{3
  f.i <- svalue(f.gtable, index = TRUE)
  ws$delete_f(f.i)
  update_f.df()
  p.modified <<- TRUE
}
keep_fit_handler <- function(h, ...) { # {{{3
#   f.cur <<- as.character(length(f) + 1)
#   f[[f.cur]] <<- ftmp
#   s[[f.cur]] <<- stmp
#   update_f.df()
#   f.gtable[,] <<- f.df
#   delete(f.gg.plotopts, f.gg.po.obssel)
#   f.gg.po.obssel <<- gcheckboxgroup(names(ftmp$mkinmod$spec), 
#                                     cont = f.gg.plotopts, 
#                                     checked = TRUE)
#   delete(f.gg.buttons, get.initials.gc)
#   get.initials.gc <<- gcombobox(paste("Fit", f.df$Fit), 
#                                 cont = f.gg.buttons)
}
get_Parameters <- function(stmp, optimised) # {{{3
{
#   pars <- rbind(stmp$start[1:2], stmp$fixed)

#   pars$fixed <- c(rep(FALSE, length(stmp$start$value)),
#                   rep(TRUE, length(stmp$fixed$value)))
#   pars$name <- rownames(pars)
#   Parameters <- data.frame(Name = pars$name,
#                            Type = pars$type,
#                            Initial = pars$value,
#                            Fixed = pars$fixed,
#                            Optimised = as.numeric(NA))
#   Parameters <- rbind(subset(Parameters, Type == "state"),
#                       subset(Parameters, Type == "deparm"))
#   rownames(Parameters) <- Parameters$Name
#   if (optimised) {
#     Parameters[rownames(stmp$bpar), "Optimised"] <- stmp$bpar[, "Estimate"]
#   }
#   return(Parameters)
}
show_plot <- function(type, default = FALSE) {
#   Parameters <- f.gg.parms[,]
#   Parameters.de <- subset(Parameters, Type == "deparm", type)
#   stateparms <- subset(Parameters, Type == "state")[[type]]
#   deparms <- as.numeric(Parameters.de[[type]])
#   names(deparms) <- rownames(Parameters.de)
#   if (type == "Initial" & default == FALSE) {
#     ftmp <<- suppressWarnings(mkinfit(ftmp$mkinmod, 
#                                       override(ds[[ds.i]]$data),
#                                       parms.ini = deparms,
#                                       state.ini = stateparms, 
#                                       fixed_parms = names(deparms),
#                                       fixed_initials = names(stateparms),
#                                       err = "err", 
#                                       method.modFit = "Marq",
#                                       control.modFit = list(maxiter = 0)))
#     ftmp$ds.index <<- ds.i
#     ftmp$ds <<- ds[[ds.i]]
#   } 
#   svalue(plot.ftmp.gi) <<- plot_ftmp_png()
#   svalue(plot.confint.gi) <<- plot_confint_png()
}
# Widget setup {{{2
# Line 1 with buttons {{{3
f.buttons <- ggroup(cont = f.config, horizontal = TRUE)
f.run <- gbutton("Run fit", cont = f.buttons, handler = function(h, ...) run_fit(),
                 ext.args = list(disabled = TRUE))
f.delete <- gbutton("Delete fit", cont = f.buttons, 
  handler = delete_fit_handler, ext.args = list(disabled = TRUE))
f.keep <- gbutton("Keep fit", cont = f.buttons, handler = keep_fit_handler)
tooltip(f.keep) <- "Store the optimised model with all settings and the current dataset in the fit list"
f.keep$call_Ext("disable")

# center: Results viewer {{{1
r.viewer  <- gframe("", horizontal = FALSE, cont = center, 
                    label = "Result")
svalue(center) <- 1
# right: Viewing area {{{1
# Workflow {{{2
workflow.gg <- ggroup(cont = right, label = "Workflow", width = 480,  height = 570,
                      ext.args = list(layout = list(type="vbox", align = "center")))

workflow.png <- get_tempfile(ext = ".png")
file.copy(system.file("GUI/gmkin_workflow_434x569.png", package = "gmkin"), workflow.png)
workflow.gi <- gimage(workflow.png, size = c(434, 569), label = "Workflow", cont = workflow.gg)

# # Kinetic Data {{{3
ds.e.gdf <- gdf(ds.cur$data, label = "Data editor", name = "Kinetic data", 
                width = 488, height = 600, cont = right)

workflow.png <- get_tempfile(ext = ".png")
file.copy(system.file("GUI/gmkin_workflow_434x569.png", package = "gmkin"), workflow.png)
workflow.gi <- gimage(workflow.png, size = c(434, 569), label = "Workflow", cont = workflow.gg)
# Model Gallery {{{3
m.g.gg <- ggroup(cont = right, label = "Model gallery", width = 480,  height = 570,
                 ext.args = list(layout = list(type="vbox", align = "center")))

# Manual {{{2
gmkin_manual <- readLines(system.file("GUI/gmkin_manual.html", package = "gmkin"))
gmb_start <- grep("<body>", gmkin_manual)
gmb_end <- grep("</body>", gmkin_manual)
gmkin_manual_body <- gmkin_manual[gmb_start:gmb_end]

manual.gh <- ghtml(label = "Manual", paste0("<div class = 'manual' style = 'margin: 20px'>
<style>
.manual h1{
  font-size: 14px;
  line-height: 20px;
}
.manual h2{
  font-size: 14px;
  line-height: 20px;
}
.manual h3{
  font-size: 12px;
  line-height: 18px;
}
.manual ul{
  font-size: 12px;
  line-height: 12px;
}
.manual li{
  font-size: 12px;
  line-height: 12px;
}
</style>
", paste(gmkin_manual_body, collapse = '\n'), "
</div>"), width = 460, cont = right)

# Changes {{{2
gmkin_news <- markdownToHTML(system.file("NEWS.md", package = "gmkin"), 
                             fragment.only = TRUE,
                             )

changes.gh <- ghtml(label = "Changes", paste0("<div class = 'news' style = 'margin: 20px'>
<style>
.news h1{
  font-size: 14px;
  line-height: 20px;
}
.news h2{
  font-size: 14px;
  line-height: 20px;
}
.news h3{
  font-size: 12px;
  line-height: 18px;
}
.news ul{
  font-size: 12px;
  line-height: 12px;
}
.news li{
  font-size: 12px;
  line-height: 12px;
}
</style>
", gmkin_news, "
</div>"), width = 460, cont = right)

# Things to do in the end
# Update meta objects and their depending widgets
svalue(right) <- 1
update_p.df()
# vim: set foldmethod=marker ts=2 sw=2 expandtab: {{{1