From 941c810ca74b664072ddde601b3354014321e437 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Fri, 25 Oct 2013 21:48:13 +0000
Subject: A new layout for the GUI and an update of the staticdocs, as I just
 uploaded 0.9-22 for publication on CRAN

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@125 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
 inst/GUI/mkinGUI.R | 445 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 445 insertions(+)
 create mode 100644 inst/GUI/mkinGUI.R

(limited to 'inst/GUI')

diff --git a/inst/GUI/mkinGUI.R b/inst/GUI/mkinGUI.R
new file mode 100644
index 0000000..cf66b01
--- /dev/null
+++ b/inst/GUI/mkinGUI.R
@@ -0,0 +1,445 @@
+# $Id: mkinGUI.R 122 2013-10-21 20:19:57Z jranke $ {{{1
+
+# gWidgetsWWW2 GUI for mkin
+
+# Copyright (C) 2013 Johannes Ranke
+# Contact: jranke@uni-bremen.de, johannesranke@eurofins.com
+
+# This file is part of the R package mkin
+
+# mkin 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/>
+require(mkin) # {{{1
+# Set the GUI title and create the basic widget layout {{{1
+w      <- gwindow("Browser based GUI for kinetic evaluations using mkin")
+sb     <- gstatusbar("Powered by gWidgetsWWW2 and Rook", cont = w)
+pg     <- gpanedgroup(cont = w, default.size = 400)
+center <- gnotebook(cont = pg)
+left   <- gvbox(cont = pg)
+# Helper functions {{{1
+# Override function for making it possible to override original data in the GUI {{{2
+override <- function(d) {
+  data.frame(name = d$name, time = d$time, 
+             value = ifelse(is.na(d$override), d$value, d$override),
+             err = d$err)
+}
+# Set default values for project data {{{1
+# Initial project file name {{{2
+project_file <- "mkin_FOCUS_2006.RData"
+# Initial studies {{{2
+studies.df <- data.frame(Index = as.integer(1), 
+                         Author = "FOCUS kinetics workgroup",
+                         Year = "2006", 
+                         Title = "FOCUS Kinetics",
+                         stringsAsFactors = FALSE)
+# Initial datasets {{{2
+ds <- list()
+observed.all <- vector()
+for (i in 1:2) {
+  ds.letter = LETTERS[i + 2]
+  ds.index <- as.character(i)
+  ds.name = paste0("FOCUS_2006_", ds.letter)
+  ds[[ds.index]] <- list(
+    study_nr = 1,
+    title = paste("FOCUS example dataset", ds.letter),
+    sampling_times = unique(get(ds.name)$time),
+    time_unit = "",
+    observed = as.character(unique(get(ds.name)$name)),
+    unit = "% AR",
+    replicates = 1,
+    data = get(ds.name)
+  )
+  ds[[ds.index]]$data$name <- as.character(ds[[ds.index]]$data$name)
+  ds[[ds.index]]$data$override = as.numeric(NA)
+  ds[[ds.index]]$data$err = 1
+}
+# Dataframe with datasets for selection {{{2
+update_ds.df <- function() {
+  ds.n <- length(ds)
+  ds.df <<- data.frame(Index = 1:ds.n, 
+                       Title = character(ds.n),
+                       Study = character(ds.n), 
+                       stringsAsFactors = FALSE)
+  for (i in 1:ds.n)
+  {
+    ds.index <- names(ds)[[i]]
+    ds.df[i, "Title"] <<- ds[[ds.index]]$title
+    ds.df[i, "Study"] <<- ds[[ds.index]]$study_nr
+    observed = as.character(unique(ds[[ds.index]]$data$name))
+    observed.all <<- union(observed, observed.all)
+  }
+}
+ds.df <- data.frame()
+update_ds.df()
+ds.cur = "1"
+# Initial models {{{2
+m <- list()
+m[["1"]] <- mkinmod(parent = list(type = "SFO"))
+m[["1"]]$name = "SFO"
+m[["2"]] <- mkinmod(parent = list(type = "FOMC"))
+m[["2"]]$name = "FOMC"
+m[["3"]] <- mkinmod(parent = list(type = "DFOP"))
+m[["3"]]$name = "DFOP"
+m[["4"]] <- mkinmod(parent = list(type = "SFO", to = "m1"),
+                          m1 = list(type = "SFO"),
+                          use_of_ff = "max")
+m[["4"]]$name = "SFO_SFO"
+# Dataframe with models for selection {{{2
+update_m.df <- function() {
+  m.n <- length(m)
+  m.df <<- data.frame(Index = 1:m.n, 
+                      Name = character(m.n),
+                      stringsAsFactors = FALSE)
+  for (i in 1:m.n) {
+    m.index <- names(m)[[i]]
+    m.df[i, "Name"] <<- m[[m.index]]$name
+  }
+}
+m.df <- data.frame()
+update_m.df()
+m.cur = "1"
+# Widgets and handlers for project data {{{1
+prg <- gexpandgroup("Project file management", cont = left, horizontal = FALSE)
+visible(prg) <- FALSE
+# Project data management handler functions {{{2
+upload_file_handler <- function(h, ...)
+{
+  tmpfile <- normalizePath(svalue(h$obj), winslash = "/")
+  try(load(tmpfile))
+  project_file <<- pr.gf$filename
+  svalue(pr.ge) <- project_file
+  studies.gdf[,] <- studies.df 
+  ds.cur <<- "1"
+  ds <<- ds
+  update_ds.df()
+  ds.gtable[,] <- ds.df
+  update_ds_editor()
+  m.cur <<- "1"
+  m <<- m
+  update_m.df()
+  m.gtable[,] <- m.df
+  update_m_editor()
+}
+save_to_file_handler <- function(h, ...)
+{
+   studies.df <- data.frame(studies.gdf[,], stringsAsFactors = FALSE)
+   save(studies.df, ds, m, file = project_file)
+   galert(paste("Saved project contents to", project_file), parent = w)
+}
+change_project_file_handler = function(h, ...) {
+  project_file <<- as.character(svalue(h$obj))
+}
+# Project data management GUI elements {{{2
+pr.gf <- gfile(text = "Select project file", cont = prg,
+               handler = upload_file_handler)
+pr.ge <- gedit(project_file, cont = prg, 
+               handler = change_project_file_handler)
+# The save button is always visible {{{1
+gbutton("Save current project contents", cont = left,
+        handler = save_to_file_handler)
+
+# GUI widgets and a function for Studies {{{1
+stg <- gexpandgroup("Studies", cont = left)
+visible(stg) <- FALSE
+update_study_selector <- function(h, ...) {
+  delete(ds.e.1, ds.study.gc)
+  ds.study.gc <<- gcombobox(paste("Study", studies.gdf[,1]), cont = ds.e.1) 
+  svalue(ds.study.gc, index = TRUE) <- ds[[ds.cur]]$study_nr
+}
+studies.gdf <- gdf(studies.df, name = "Edit studies in the project",
+                   width = 390, height = 200, cont = stg)
+studies.gdf$set_column_width(1, 35)
+studies.gdf$set_column_width(2, 150)
+studies.gdf$set_column_width(3, 40)
+addHandlerChanged(studies.gdf, update_study_selector)
+# Datasets and models {{{1
+dsm <- gframe("Datasets and models", cont = left, horizontal = FALSE)
+# Dataset table with handler {{{2
+ds.switcher <- function(h, ...) {
+  ds.cur <<- as.character(svalue(h$obj))
+  update_ds_editor()
+  svalue(center) <- 1
+}
+ds.gtable <- gtable(ds.df, width = 390, multiple = TRUE, cont = dsm)
+addHandlerDoubleClick(ds.gtable, ds.switcher)
+size(ds.gtable) <- list(columnWidths = c(40, 300, 40))
+
+# Model table with handler {{{2
+m.switcher <- function(h, ...) {
+  m.cur <<- as.character(svalue(h$obj))
+  update_m_editor()
+  svalue(center) <- 2
+}
+m.gtable <- gtable(m.df, width = 390, multiple = TRUE, cont = dsm)
+addHandlerDoubleClick(m.gtable, m.switcher)
+size(m.gtable) <- list(columnWidths = c(40, 340))
+
+# Dataset editor {{{1
+ds.editor <- gframe("Dataset 1", horizontal = FALSE, cont = center, label = "Dataset editor")
+# Handler functions {{{3
+copy_dataset_handler <- function(h, ...) {
+  ds.old <- ds.cur
+  ds.cur <<- as.character(1 + length(ds))
+  svalue(ds.editor) <- paste("Dataset", ds.cur)
+  ds[[ds.cur]] <<- ds[[ds.old]]
+  update_ds.df()
+  ds.gtable[,] <- ds.df
+}
+ 
+delete_dataset_handler <- function(h, ...) {
+  ds[[ds.cur]] <<- NULL
+  names(ds) <<- names(plots) <<- names(prows) <<- as.character(1:length(ds))
+  ds.cur <<- names(ds)[[1]]
+  update_ds.df()
+  ds.gtable[,] <- ds.df
+  update_ds_editor()
+}
+ 
+new_dataset_handler <- function(h, ...) {
+  ds.cur <<- as.character(1 + length(ds))
+  ds[[ds.cur]] <<- list(
+                        study_nr = 1,
+                        title = "",
+                        sampling_times = c(0, 1),
+                        time_unit = "NA",
+                        observed = "parent",
+                        unit = "NA",
+                        replicates = 1,
+                        data = data.frame(
+                                          name = "parent",
+                                          time = c(0, 1),
+                                          value = c(100, NA),
+                                          override = "NA",
+                                          err = 1,
+                                          stringsAsFactors = FALSE
+                                          )
+                        )
+  update_ds.df()
+  ds.gtable[,] <- ds.df
+  update_ds_editor()
+}
+
+empty_grid_handler <- function(h, ...) {
+  obs <- strsplit(svalue(ds.e.obs), ", ")[[1]]
+  sampling_times <- strsplit(svalue(ds.e.st), ", ")[[1]]
+  replicates <- as.numeric(svalue(ds.e.rep))
+  new.data = data.frame(
+    name = rep(obs, each = replicates * length(sampling_times)),
+    time = rep(sampling_times, each = replicates, times = length(obs)),
+    value = NA,
+    override = NA,
+    err = 1
+  )
+  ds.e.gdf[,] <- new.data
+}
+
+save_ds_changes_handler <- function(h, ...) {
+  ds[[ds.cur]]$title <<- svalue(ds.title.ge)
+  ds[[ds.cur]]$study_nr <<- as.numeric(gsub("Study ", "", svalue(ds.study.gc)))
+  update_ds.df()
+  ds.gtable[,] <- ds.df
+  tmpd <- ds.e.gdf[,]
+  ds[[ds.cur]]$data <<- tmpd
+  ds[[ds.cur]]$sampling_times <<- sort(unique(tmpd$time))
+  ds[[ds.cur]]$time_unit <<- svalue(ds.e.stu)
+  ds[[ds.cur]]$observed <<- unique(tmpd$name)
+  ds[[ds.cur]]$unit <<- svalue(ds.e.obu)
+  ds[[ds.cur]]$replicates <<- max(aggregate(tmpd$time, 
+                                            list(tmpd$time, tmpd$name), length)$x)
+  update_ds_editor()
+  update_plot()
+}
+ 
+# Widget setup {{{3
+# Line 1 {{{4
+ds.e.1 <- ggroup(cont = ds.editor, horizontal = TRUE)
+glabel("Title: ", cont = ds.e.1) 
+ds.title.ge <- gedit(ds[[ds.cur]]$title, cont = ds.e.1) 
+glabel(" from ", cont = ds.e.1) 
+ds.study.gc <- gcombobox(paste("Study", studies.gdf[,1]), cont = ds.e.1) 
+
+# Line 2 {{{4
+ds.e.2 <- ggroup(cont = ds.editor, horizontal = TRUE)
+gbutton("Copy dataset", cont = ds.e.2, handler = copy_dataset_handler)
+gbutton("Delete dataset", cont = ds.e.2, handler = delete_dataset_handler)
+gbutton("New dataset", cont = ds.e.2, handler = new_dataset_handler)
+
+# Line 3 with forms {{{4
+ds.e.forms <- ggroup(cont= ds.editor, horizontal = TRUE)
+
+ds.e.3a <- gvbox(cont = ds.e.forms)
+ds.e.3a.gfl <- gformlayout(cont = ds.e.3a)
+ds.e.st  <- gedit(paste(ds[[ds.cur]]$sampling_times, collapse = ", "),
+                  width = 40,
+                  label = "Sampling times", 
+                  cont = ds.e.3a.gfl)
+ds.e.stu <- gedit(ds[[ds.cur]]$time_unit, 
+                  width = 20,
+                  label = "Unit", cont = ds.e.3a.gfl)
+ds.e.rep <- gedit(ds[[ds.cur]]$replicates, 
+                  width = 20,
+                  label = "Replicates", cont = ds.e.3a.gfl)
+
+ds.e.3b <- gvbox(cont = ds.e.forms)
+ds.e.3b.gfl <- gformlayout(cont = ds.e.3b)
+ds.e.obs <- gedit(paste(ds[[ds.cur]]$observed, collapse = ", "),
+                  width = 50,
+                  label = "Observed", cont = ds.e.3b.gfl)
+ds.e.obu <- gedit(ds[[ds.cur]]$unit,
+                  width = 20, label = "Unit", 
+                  cont = ds.e.3b.gfl)
+gbutton("Generate empty grid for kinetic data", cont = ds.e.3b, 
+        handler = empty_grid_handler)
+
+# Save button {{{4
+gbutton("Save changes", cont = ds.editor, handler = save_ds_changes_handler)
+
+# Kinetic Data {{{4
+ds.e.gdf <- gdf(ds[[ds.cur]]$data, name = "Kinetic data", 
+                width = 500, height = 700, cont = ds.editor)
+ds.e.gdf$set_column_width(2, 70)
+
+# Update the dataset editor {{{3
+update_ds_editor <- function() {
+  svalue(ds.editor) <- paste("Dataset", ds.cur)
+  svalue(ds.title.ge) <- ds[[ds.cur]]$title
+  svalue(ds.study.gc, index = TRUE) <- ds[[ds.cur]]$study_nr
+
+  svalue(ds.e.st) <- paste(ds[[ds.cur]]$sampling_times, collapse = ", ")
+  svalue(ds.e.stu) <- ds[[ds.cur]]$time_unit
+  svalue(ds.e.obs) <- paste(ds[[ds.cur]]$observed, collapse = ", ")
+  svalue(ds.e.obu) <- ds[[ds.cur]]$unit
+  svalue(ds.e.rep) <- ds[[ds.cur]]$replicates
+
+  ds.e.gdf[,] <- ds[[ds.cur]]$data
+}
+# Model editor {{{1
+m.editor <- gframe("Model 1", horizontal = FALSE, cont = center, label = "Model editor")
+# Handler functions {{{3
+copy_model_handler <- function(h, ...) {
+  m.old <- m.cur
+  m.cur <<- as.character(1 + length(m))
+  svalue(m.editor) <- paste("Model", m.cur)
+  m[[m.cur]] <<- m[[m.old]]
+  update_m.df()
+  m.gtable[,] <- m.df
+}
+ 
+delete_model_handler <- function(h, ...) {
+  m[[m.cur]] <<- NULL
+  names(m) <<- as.character(1:length(m))
+  m.cur <<- "1"
+  update_m.df()
+  m.gtable[,] <- m.df
+  update_m_editor()
+}
+
+add_observed_handler <- function(h, ...) {
+  obs.i <- length(m.e.rows) + 1
+  m.e.rows[[obs.i]] <<- ggroup(cont = m.editor, horizontal = TRUE)
+  m.e.obs[[obs.i]] <<- gcombobox(observed.all, selected = obs.i, 
+                                cont = m.e.rows[[obs.i]])
+  m.e.type[[obs.i]] <<- gcombobox(c("SFO", "FOMC", "DFOP", "HS", "SFORB"),
+                                 cont = m.e.rows[[obs.i]])
+  svalue(m.e.type[[obs.i]]) <- "SFO"
+  glabel("to", cont = m.e.rows[[obs.i]]) 
+  m.e.to[[obs.i]] <<- gedit("", cont = m.e.rows[[obs.i]])
+  m.e.sink[[obs.i]] <<- gcheckbox("Path to sink", 
+                                  checked = TRUE, cont = m.e.rows[[obs.i]]) 
+  gbutton("Remove compound", handler = remove_compound_handler, 
+          action = obs.i, cont = m.e.rows[[obs.i]])
+}
+
+remove_compound_handler <- function(h, ...) {
+  m[[m.cur]]$spec[[h$action]] <<- NULL
+  update_m_editor()
+}
+
+save_m_changes_handler <- function(h, ...) {
+  spec <- list()
+  for (obs.i in 1:length(m.e.rows)) {
+    spec[[obs.i]] <- list(type = svalue(m.e.type[[obs.i]]),
+                          to = svalue(m.e.to[[obs.i]]),
+                          sink = svalue(m.e.sink[[obs.i]]))
+    if(spec[[obs.i]]$to == "") spec[[obs.i]]$to = NULL
+    names(spec)[[obs.i]] <- svalue(m.e.obs[[obs.i]])
+  }
+  m[[m.cur]] <<- mkinmod(use_of_ff = svalue(m.ff.gc), 
+                         speclist = spec)
+  m[[m.cur]]$name <<- svalue(m.name.ge) 
+  update_m.df()
+  m.gtable[,] <- m.df
+}
+ 
+# Widget setup {{{3
+m.e.0 <- ggroup(cont = m.editor, horizontal = TRUE)
+glabel("Model name: ", cont = m.e.0) 
+m.name.ge <- gedit(m[[m.cur]]$name, cont = m.e.0) 
+glabel("Use of formation fractions: ", cont = m.e.0) 
+m.ff.gc <- gcombobox(c("min", "max"), cont = m.e.0)
+svalue(m.ff.gc) <- m[[m.cur]]$use_of_ff
+
+# Model handling buttons {{{4
+m.e.b <- ggroup(cont = m.editor, horizontal = TRUE)
+gbutton("Copy model", cont = m.e.b, handler = copy_model_handler)
+gbutton("Delete model", cont = m.e.b, handler = delete_model_handler)
+gbutton("Add transformation product", cont = m.e.b, 
+        handler = add_observed_handler)
+gbutton("Save changes", cont = m.e.b, handler = save_m_changes_handler)
+
+
+m.observed <- names(m[[m.cur]]$spec)
+m.e.rows <- m.e.obs <- m.e.type <- m.e.to <- m.e.sink <- list()
+obs.to <- ""
+
+# Show the model specification {{{4
+show_m_spec <- function() {
+  for (obs.i in 1:length(m.observed)) {
+    m.e.rows[[obs.i]] <<- ggroup(cont = m.editor, horizontal = TRUE)
+    m.e.obs[[obs.i]] <<- gcombobox(observed.all, selected = obs.i, 
+                                  cont = m.e.rows[[obs.i]])
+    m.e.type[[obs.i]] <<- gcombobox(c("SFO", "FOMC", "DFOP", "HS", "SFORB"),
+                                   cont = m.e.rows[[obs.i]])
+    svalue(m.e.type[[obs.i]]) <<- m[[m.cur]]$spec[[obs.i]]$type
+    glabel("to", cont = m.e.rows[[obs.i]]) 
+    obs.to <<- ifelse(is.null(m[[m.cur]]$spec[[obs.i]]$to), "",
+                 m[[m.cur]]$spec[[obs.i]]$to)
+    m.e.to[[obs.i]] <<- gedit(obs.to, cont = m.e.rows[[obs.i]])
+    m.e.sink[[obs.i]] <<- gcheckbox("Path to sink", checked = m[[m.cur]]$spec[[obs.i]]$sink,
+              cont = m.e.rows[[obs.i]]) 
+    if (obs.i > 1) {
+      gbutton("Remove compound", handler = remove_compound_handler, 
+              action = obs.i, cont = m.e.rows[[obs.i]])
+    }
+  }
+}
+show_m_spec()
+
+# Update the model editor {{{3
+update_m_editor <- function() {
+  svalue(m.editor) <- paste("Model", m.cur)
+  svalue(m.name.ge) <- m[[m.cur]]$name
+  svalue(m.ff.gc) <- m[[m.cur]]$use_of_ff
+  for (oldrow.i in 1:length(m.e.rows)) {
+    delete(m.editor, m.e.rows[[oldrow.i]])
+  }
+  m.observed <<- names(m[[m.cur]]$spec)
+  m.e.rows <<- m.e.obs <<- m.e.type <<- m.e.to <<- m.e.sink <<- list()
+  show_m_spec()
+}
+
+# 3}}}
+# 2}}}
+# 1}}}
+
+# vim: set foldmethod=marker ts=2 sw=2 expandtab:
-- 
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