R/gui.R
In sebkopf/idp: Process compound specific D/H isotope data collected with isodat
##################
# Info messaging #
##################
# show an info message
# type - styling of the mssage, info, error, question, warning are the standard ones
# timer - time in seconds until message disappears automatically
# okButton - whether there is an ok button or not
IDP.showInfo<-function(idp, msg, type="question", timer=2, okButton=TRUE) {
idp$gui$infoBar$setMessageType(type)
idp$gui$infoLabel$setText(msg)
idp$gui$infoBar$show()
if (!okButton)
idp$gui$infoOkButton$hide()
else
idp$gui$infoOkButton$show()
if (!is.null(timer)) {
Sys.sleep(timer)
IDP.hideInfo(idp)
}
}
# hide info bar
IDP.hideInfo<-function(idp) {
idp$gui$infoBar$hide()
}
############
# Main GUI #
############
# launch the user interface
IDP.gui<-function(idp) {
# show a small loading window
load_win <- gwindow("Loading IDP...", width=400, height=100, visible=FALSE)
load_grp <- ggroup(horizontal=FALSE, expand=TRUE, cont=load_win)
addSpring(load_grp, expand=T)
glabel("Loading User Interface, please wait...", cont=load_grp)
addSpring(load_grp, expand=T)
visible(load_win, TRUE)
Sys.sleep(2)
# keep track of whether the DSQDP is running
IDP.running <<- TRUE
### main window
idp$gui$win <- win.init(paste("Isodat Data Processor - version", packageVersion('idp')),
width=1280, height=750, modal = idp$gui$modal, parent = idp$gui$parent)
# if (idp$gui$modal) {
# message("\nStarting IDP in modal mode (started via script).\n")
# idp$gui$win<-gbasicdialog(title=paste("Isodate File Processor - version", packageVersion('idp')), do.buttons=FALSE, visible=FALSE, parent=idp$gui$parent)
# size(idp$gui$win) <- c(1280, 750)
# } else {
# message("\nStarting IDP in window mode.\n")
# idp$gui$win<-gwindow(paste("Isodate File Processor - version", packageVersion('idp')), width=1280, height=750, visible=FALSE, parent=idp$gui$parent)
# }
# make sure to kill modal run by setting running flag back to FALSE
addHandlerDestroy(idp$gui$win, handler=function(h,...) { message("\nGoodbye!!"); IDP.running <<- FALSE })
### storing settings for easier modification
tag(idp$gui$win, "settings")<-idp$settings
### major divisions
wingrp<-ggroup(horizontal=FALSE, expand=TRUE, cont=idp$gui$win, spacing=0)
if (idp$gui$modal)
parent <- getToolkitWidget(wingrp) # get automatic toplevel gtkHBox generated by dialog
else
parent <- getToolkitWidget(wingrp)$getParent() # get automatic toplevel gtkHBox generated by gwindow
parent['border-width']<-0 # remove border
idp$gui$navgrp<-ggroup(horizontal=FALSE, cont=wingrp, spacing=0) # navigation group
# left top
glt<-ggroup(horizontal=FALSE, expand=TRUE) # left column file browser group
# left bottom
glb<-ggroup(horizontal=FALSE, expand=TRUE) # left column for file info
glbGTK<-getToolkitWidget(glb) # gtk object
glbGTK['border-width']<-5 # border with
# right top
grt<-ggroup(horizontal=TRUE, expand=TRUE) # right top
plot.grp<-ggroup(horizontal=FALSE, expand=TRUE, container=grt) # plot grp in right top
# right bottom
grb<-ggroup(horizontal=TRUE, expand=TRUE) # right bottom
tag(idp$gui$win, "tableGrp")<-ggroup(horizontal=FALSE, expand=TRUE, container=grb) # table grp in bottom right
idp$gui$gl<-gpanedgroup(glt, glb, horizontal=FALSE, expand=TRUE) # left column
idp$gui$gr<-gpanedgroup(grt, grb, horizontal=FALSE, expand=TRUE) # right column
idp$gui$gall<-gpanedgroup(idp$gui$gl, idp$gui$gr, horizontal=TRUE, container=wingrp, expand=TRUE) # total window group
### files browser
tag(idp$gui$win, "fileBrowserParentGrp")<-glt
tag(idp$gui$win, "fileBrowserGrp")<-NULL
# all the items of the file browser
fileBrowser.items <- function(path = NULL, user.data=NULL) {
topleveldir <- is.null(path)
if (topleveldir)
path <- tag(idp$gui$win, "settings")$fileDirectory # start with file directory from the settings
files <- file.info(dir(path=path, full.names=TRUE))[,c(1,2,3)] # get all files and folders
files <- data.frame(Name=dir(path=path), Dir=files[,2], stringsAsFactors=FALSE)
files <- files[union(which(files$Dir), grep("\\.cf$", files$Name)),] # only folders and .cf files
files <- files[order(-files$Dir, files$Name),] # sort by folder vs file and then name
if (topleveldir) # add "..." at the beginning (FIXME: could make sure that it's not added if at root but too lazy now)
files <- rbind(data.frame(Name="...", Dir=FALSE), files)
return(files)
}
# functions to determine which items have sub items and which icons to use
fileBrowser.hasOffspring <- function(children,user.data=NULL, ...)return(children$Dir) # which items have subdirectories
fileBrowser.icons <- function(children,user.data=NULL, ...) {
x <- rep("gtk-new", length=nrow(children))
x[which(children$Name=="...")] <- "gtk-directory" # top level folder
x[children$Dir] <- "gtk-directory" # real folders
return(x)
}
# function to remake the file tree when switching folders (FIXME: somehow looses ability for tree expansion...maybe something about how the tree is added?)
fileBrowser.gui<-function() {
if (!is.null(tag(idp$gui$win, "fileBrowserGrp")))
delete(tag(idp$gui$win, "fileBrowserParentGrp"), tag(idp$gui$win, "fileBrowserGrp"))
tag(idp$gui$win, "fileBrowserGrp") <- ggroup(expand=TRUE)
add(tag(idp$gui$win, "fileBrowserParentGrp"), tag(idp$gui$win, "fileBrowserGrp"), expand=TRUE)
tree<-gtree(fileBrowser.items, fileBrowser.hasOffspring, icon.FUN = fileBrowser.icons, container=tag(idp$gui$win, "fileBrowserGrp"), expand=TRUE, handler=function(h,...) {
if (is.null(subpath <- svalue(h$obj[]))) {
path <- IDP.getSettings(idp, "fileDirectory")
file <- svalue(h$obj)
} else {
path <- file.path(IDP.getSettings(idp, "fileDirectory"), do.call("file.path", args=as.list(subpath[-length(subpath)])))
file <- subpath[length(subpath)]
}
newpath <- file.path(path, file) # assemble new path
if (identical(file, "...")) { # except: top level directory
pathparts <- strsplit(path, .Platform$file.sep)[[1]]
newpath <- do.call("file.path", args=as.list(pathparts[-length(pathparts)]))
}
#message(newpath, "\n", path, "\n", file)
if (file.info(newpath)$isdir) { # open directory
IDP.setSettings(idp, list(fileDirectory = newpath))
fileBrowser.gui()
} else # open file
IDP.openIsodatFile(idp, path, file)
})
}
# --> file browser initialization is at the end because it needs other idp objects to be fully initialized
### file info group
idp$gui$fileInfo<-list()
idp$gui$fileInfo.nb<-gnotebook(cont = glb, expand=TRUE)
fileInfo.layout <- glayout(cont = idp$gui$fileInfo.nb, expand=TRUE, label="File Info")
fileInfo.layout[1, 1] <- "File:"
fileInfo.layout[1, 2] <- (idp$gui$fileInfo$Filename <- glabel("", cont=fileInfo.layout))
fileInfo.layout[2, 1] <- "GC:"
fileInfo.layout[2, 2] <- (idp$gui$fileInfo$GCprogram <- glabel("", cont=fileInfo.layout))
fileInfo.layout[3, 1] <- "AS:"
fileInfo.layout[3, 2] <- (idp$gui$fileInfo$ASprogram <- glabel("", cont=fileInfo.layout))
fileInfo.layout[4, 1] <- "MS:"
fileInfo.layout[4, 2] <- (idp$gui$fileInfo$MSprogram <- glabel("", cont=fileInfo.layout))
fileInfo.layout[5, 1] <- "H3:"
fileInfo.layout[5, 2] <- (idp$gui$fileInfo$H3factor <- glabel("", cont=fileInfo.layout))
### file graph
idp$gui$info.graph <- ggraphics(container=idp$gui$fileInfo.nb, label="Refs", expand=TRUE)
idp$gui$data.graph <- ggraphics(container=idp$gui$fileInfo.nb, label="Data", expand=TRUE)
### plot grp
idp$gui$pn <- pn.GUI(plot.grp, idp$gui$win, enablePlotLabel=FALSE, enableMenuButtons=FALSE, startWithTab=FALSE,
plotObjLoadHandler=function(obj) IDP.loadIsodatFileTab(idp, obj$plotinfo),
plotEventHandlers=list(
Changed = function(h,...) IDP.plotClickHandler(idp, h),
Doubleclick = function(h,...) IDP.plotDoubleClickHandler(idp, h),
Rightclick = function(h,...) IDP.plotRightClickHandler(idp, h)))
### table grp
tag(idp$gui$win, "dataTable") <- gtable(IDP.getEmptyPeakTable(idp), expand=TRUE, cont=tag(idp$gui$win, "tableGrp"))
data_table_click_handler <- function(h,...) {
if ( length(svalue(h$obj, index = TRUE)) > 0 ) IDP.plot(idp) # replot to highlight the value
}
addHandlerClicked( tag(idp$gui$win, "dataTable"), handler = data_table_click_handler)
### menu and toolbar navigation actions
nav.xml <- IDP.getNavXML()
nav.actions <-
list(## name, icon, label , accelerator , tooltip , callback
list ("IDP" , NULL , "_IDP" , NULL , NULL , NULL ) ,
list ("SaveToWorkspace" , "gtk-home" , "Save To Workspace" , "<ctrl>H" ,"Save settings to workspace" , function(...) { # include also data once ready
IDP.showInfo(idp, "Saving to workspace...", timer=1, okButton=FALSE)
IDP.save(idp)
IDP.showInfo(idp, "Isodat File Processor settings succesfully saved to workspace.", timer=2, okButton=FALSE)
} ) ,
list ("Quit", "gtk-quit", "Quit", NULL, "Quit program", function(...) { if (gconfirm("Are you sure you want to quit?")) dispose(idp$gui$win) } ),
list ("File" , NULL , "_File" , NULL , NULL , NULL ) ,
list ("OpenFile" , "gtk-open" , "Open File" , "<ctrl>O" ,"Open isodat file" , function(...) message("sorry, file selection dialog not implemented yet") ) ,
list ("CloseFile" , "gtk-close" , "Close File" , "<ctrl>W" ,"Close isodat file" , idp$gui$pn$actions$aClosePlot$handler ) ,
list ("CloseAll" , "gtk-stop" , "Close all Files" , "<ctrl><shift>W" ,"Close all isodat files" , function(...) gmessage("sorry, not implemented yet") ) ,
list ("ExportExcel" , "gtk-save-as" , "Export to Excel" , "<ctrl>X" , "Export raw data and peak table to excel" , function(...) idp.exportFileToExcel(idp) ) ,
list ("ExportAll" , "gtk-harddisk" , "Export all to Excel" , "<ctrl><shift>X" , "Export peak table for all files" , function(...) idp.exportAllPeakTablesToExcel(idp, saveAll=TRUE) ) ,
list ("Plot" , NULL , "_Chrom" , NULL , NULL , NULL ) ,
list ("SavePlot", "gtk-save-as", "Save as PDF", "<ctrl>S", "Save chromatogram as PDF", idp$gui$pn$actions$aSavePlot$handler ),
list ("SaveAll", "gtk-harddisk", "Save all", "<ctrl><shift>S", "Save all chromatograms as PDFs", idp$gui$pn$actions$aSaveAll$handler ),
list ("PrintPlot", "gtk-print", "Print", NULL, "Print chromatogram", idp$gui$pn$actions$aPrintPlot$handler ),
list ("Help" , "gtk-info" ,"Help" , NULL , NULL , function(...) gmessage("sorry, not implemented yet") ) ,
list ("View" , NULL , "_View" , NULL , NULL , NULL ) ,
list ("ZoomFull", "gtk-zoom-fit", "Unzoom", NULL, "Unzoom", function(h,...) IDP.zoomReset(idp) ),
list ("ZoomBack", "gtk-undo", "Undo Zoom", "<ctrl>Z", "Return to previous zoom", function(h,...) IDP.zoomBack(idp) ),
list ("ZoomIn", "gtk-zoom-in", "Zoom in", "<ctrl>P", "Zoom in", function(h,...) IDP.zoomIn(idp) ), # fix me, bertter short cuts?
list ("ZoomOut", "gtk-zoom-out", "Zoom out", "<ctrl>M", "Zoom out", function(h,...) IDP.zoomOut(idp) ), # fix me, better short cuts?
list ("MoveIntervalB", "gtk-go-back", "Move Left", "<ctrl><shift>Left", "Move visible window to the left", function (h,...) IDP.zoomMove(idp, -1)), # FIXME: shortcuts don't work
list ("MoveIntervalF", "gtk-go-forward", "Move Right", "<ctrl><shift>Right", "Move visible window to the right", function (h,...) IDP.zoomMove(idp, +1)), # FIXME: shortcuts don't work
list ("SetAxes", "gtk-page-setup", "Set Axes", NULL, "Set axis coordinates", function(h,...) gmessage("not implemented yet") ), # fix me, better short cuts?
list ("DataTable" , NULL , "_Data" , NULL , NULL , NULL ) ,
list ("StdsCalc" , NULL , "_Standards" , NULL , NULL , NULL ) ,
list ("Mode" , NULL , "_Mode" , NULL , NULL , NULL ) ,
list ("Settings" , NULL , "_Settings" , NULL , NULL , NULL ) ,
list ("XUnits" , NULL , "_X-axis Units" , NULL , NULL , NULL ) ,
list ("PlotOptions" , NULL , "_Plot Options" , NULL , NULL , NULL ) ,
list ("EditSettings" , "gtk-preferences" , "_Edit Settings" , NULL , NULL , function(...) {gmessage("no editable settings implemented yet, sorry")} ) ,
list ("TableColumns", "gtk-properties", "_Table Columns", NULL, "Select which peak table columns are displayed", function(...) {
dlg <- gbasicdialog(title="Select visible columns for the peak table", handler = function(h,...) {
tag(idp$gui$win, "settings")$peakTableColumns <- tbl[] # save updated peak table column settings
delete(tag(idp$gui$win, "tableGrp"), tag(idp$gui$win, "dataTable")) # delete previous table
tag(idp$gui$win, "dataTable")<-gtable(IDP.getEmptyPeakTable(idp), expand=TRUE, cont=tag(idp$gui$win, "tableGrp")) # remake current table
addHandlerClicked( tag(idp$gui$win, "dataTable"), handler = data_table_click_handler)
IDP.loadPeakTable(idp, pn.getAllInfo(idp$gui$pn)$peakTable)
})
size(dlg)<-c(500,500)
tbl <- table.toggleTable(ggroup(cont=dlg, expand=TRUE), tag(idp$gui$win, "settings")$peakTableColumns, "Show", invisibleColumns=c("Name", "Required", "IsodatCol"))
visible(dlg, set=TRUE) ## show dialog
}),
list ("DeletePeak" , "gtk-cancel" , "Delete Peak", "<ctrl>D", "Delete selected peak (<ctrl>D)" , function(...) { IDP.showInfo(idp, "Sorry, functionality not implemented yet", type="error", timer=2, okButton=FALSE) }),
list ("CopyTable" , "gtk-copy" , "Copy Table", "<ctrl>C", "Copy the peak table to the clipboard." , function(...) IDP.copyPeakTable(idp)),
list ("Recalculate" , "gtk-execute" , "Re-evaluate", "<ctrl>R", "Recalculate the isotopic composition based on the standards picked." , function(...) IDP.recalculatePeakTable(idp)),
list ("Revert" , "gtk-revert-to-saved" , "Revert All", NULL, "Discard all changes and return to original peak table from data file." , function(...) IDP.revertPeakTable(idp))
)
action_group <- gtkActionGroup ( "FileGroup" )
action_group$addActions( nav.actions )
### special actions
# full screen (toggle)
fullscreen_act<-gtkToggleAction("FullScreen", "Full Screen", "Make application full screen", stock.id="gtk-fullscreen")
gSignalConnect (fullscreen_act , "toggled" , function ( action ) {
if(fullscreen_act ['active'] )
getToolkitWidget(idp$gui$win)$fullscreen ( )
else
getToolkitWidget(idp$gui$win)$unfullscreen ( )
} )
action_group$addActionWithAccel(fullscreen_act, "<control>F")
# switch between multiple options [generic implementation]
optionsSwitch<-function(options, signals, action) {
for (name in names(options)) {
gSignalHandlerBlock(options[[name]], signals[[name]])
options[[name]]['active'] <- identical(name, action$name)
gSignalHandlerUnblock(options[[name]], signals[[name]])
}
return(action$name)
}
# switching x axis unit
xaxisActs<-list(
XaxisSec = gtkToggleAction("XaxisSec", "Seconds", "Show graph in seconds"),
XaxisMin = gtkToggleAction("XaxisMin", "Minutes", "Show graph in minuts")
)
xaxisSignals<-list()
for (name in names(xaxisActs)) {
xaxisSignals[[name]] <- gSignalConnect (xaxisActs[[name]] , "toggled", function(action) {
opt <- optionsSwitch(xaxisActs, xaxisSignals, action)
tag(idp$gui$win, "settings")$plotOptions$xUnits$value <- which(idp$settings$plotOptions$xUnits$ids == opt)
IDP.plot(idp) # replot
})
action_group$addAction(xaxisActs[[name]])
}
# plot options
MarkRefsAct = gtkToggleAction("MarkRefs", "Mark Reference Peaks", "Mark reference peaks with *")
MarkRefsAct['active']<-idp$settings$plotOptions$markRefs
gSignalConnect (MarkRefsAct, "toggled" , function ( action ) {
IDP.setSettings(idp, list("plotOptions.markRefs" = MarkRefsAct['active']))
IDP.plot(idp) # replot
} )
action_group$addAction(MarkRefsAct)
PeakDelimsOnAct = gtkToggleAction("PeakDelimsOn", "Show Peak Delimiters", "Show vertical lines to demarkate peaks")
PeakDelimsOnAct['active']<-idp$settings$plotOptions$edgeMarker$on
gSignalConnect (PeakDelimsOnAct, "toggled" , function ( action ) {
IDP.setSettings(idp, list("plotOptions.edgeMarker.on" = PeakDelimsOnAct['active']))
IDP.plot(idp) # replot
} )
action_group$addAction(PeakDelimsOnAct)
ApexMarkerOnAct = gtkToggleAction("ApexMarkerOn", "Show Apex Marker", "Show vertical lines to demarkate peak apex")
ApexMarkerOnAct['active']<-idp$settings$plotOptions$apexMarker$on
gSignalConnect (ApexMarkerOnAct, "toggled" , function ( action ) {
IDP.setSettings(idp, list("plotOptions.apexMarker.on" = ApexMarkerOnAct['active']))
IDP.plot(idp) # replot
} )
action_group$addAction(ApexMarkerOnAct)
# best fit (toggle)
idp$gui$bestfitActive<-gtkToggleAction("BestFit", "Best Fit", "Fit to tallest peak", stock.id="gtk-zoom-100")
gSignalConnect (idp$gui$bestfitActive , "toggled" , function ( action ) {
if (idp$gui$bestfitActive['active'])
IDP.zoomBest(idp)
} )
action_group$addActionWithAccel(idp$gui$bestfitActive, "<control>B")
# switch between modes
modeacts<-list(
ModeInfo = gtkToggleAction("ModeInfo", "Information", "Select peaks for information", stock.id="gtk-leave-fullscreen"),
ModeAdd = gtkToggleAction("ModeAdd", "Add Peak", "Add peaks", stock.id="gtk-add"),
ModeEdit = gtkToggleAction("ModeEdit", "Edit Peak", "Edit peaks", stock.id="gtk-redo"),
ModeRefs = gtkToggleAction("ModeRefs", "Choose Refs", "Choose isotopic reference peaks", stock.id="gtk-about"))
modeact_IDs<-list()
for (name in names(modeacts))
modeact_IDs[[name]] <- gSignalConnect (modeacts[[name]] , "toggled" , function(action) tag(idp$gui$win, "settings")$mode<-optionsSwitch(modeacts, modeact_IDs, action))
action_group$addActionWithAccel(modeacts$ModeInfo, "<control>I")
action_group$addActionWithAccel(modeacts$ModeAdd, "<control>A")
action_group$addActionWithAccel(modeacts$ModeEdit, "<control>E")
action_group$addActionWithAccel(modeacts$ModeRefs, NULL) #FIXME (control - C taken by copy peak table)
# switch between standards calc options
stdsCalcActs <- list(
Bracketing = gtkToggleAction("Bracketing", "Bracketing", "Use bracketing for standardization"),
Regression = gtkToggleAction("Regression", "Regression", "Use regression for standardization"))
stdsCalcSignals <- list()
for (name in names(stdsCalcActs)) {
stdsCalcSignals[[name]] <- gSignalConnect (stdsCalcActs[[name]] , "toggled" , function(action) {
tag(idp$gui$win, "settings")$stdsCalc <- optionsSwitch(stdsCalcActs, stdsCalcSignals, action)
})
action_group$addAction(stdsCalcActs[[name]])
}
### assemble menu
uimanager <- gtkUIManagerNew()
uimanager$insertActionGroup ( action_group , 0)
id <- uimanager$addUiFromString ( nav.xml )
gtkNavgrp <- getToolkitWidget(idp$gui$navgrp) # get navgrp gtk object
menubar <- uimanager$getWidget ( "/menubar" ) # menubar
gtkNavgrp$packStart ( menubar , FALSE )
toolbar <- uimanager$getWidget ( "/toolbar" ) # toolbar
gtkNavgrp$packStart ( toolbar , FALSE )
getToolkitWidget(idp$gui$win)$addAccelGroup ( uimanager$getAccelGroup ( ) ) # add keyboard triggers
### add information bar
idp$gui$infoBar <- gtkInfoBar (show=FALSE)
idp$gui$infoBar$setNoShowAll (TRUE)
idp$gui$infoLabel <- gtkLabel ( "Warning , Warning")
idp$gui$infoBar$setMessageType("question")
idp$gui$infoBar$getContentArea()$add(idp$gui$infoLabel)
idp$gui$infoOkButton <-idp$gui$infoBar$addButton(button.text = "gtk-ok", response.id = GtkResponseType['ok'])
gSignalConnect(idp$gui$infoBar, "response", function(infoBar, resp.id) IDP.hideInfo(idp))
getToolkitWidget(wingrp)$packStart(idp$gui$infoBar, expand=FALSE)
### initialize file browser (this late so it has access to the different objects created later)
fileBrowser.gui()
### make window visible after it's completely initialized
optionsSwitch(modeacts, modeact_IDs, list(name=idp$settings$mode)) # select right option from the start
optionsSwitch(xaxisActs, xaxisSignals, list(name=idp$settings$plotOptions$xUnits$ids[[idp$settings$plotOptions$xUnits$value]])) # select right xaxis from the start
optionsSwitch(stdsCalcActs, stdsCalcSignals, list(name=idp$settings$stdsCalc)) # select right option from the start
visHandler <- addHandlerFocus(idp$gui$win, handler=function(...) {
svalue(idp$gui$fileInfo.nb) <- 1
### starting plot and notebook positions
visible(idp$gui$info.graph) <- TRUE
plot.new()
text(0, 0, " ")
visible(idp$gui$data.graph) <- TRUE
plot.new()
text(0, 0, " ")
addHandlerChanged(idp$gui$fileInfo.nb, handler=function(h,...) {
if (h$pageno ==2) IDP.plotRefs(idp)
else if (h$pageno == 3) IDP.plotData(idp)
})
### divider positions
svalue(idp$gui$gl)<-IDP.getSettings(idp, "leftPane")
svalue(idp$gui$gr)<-IDP.getSettings(idp, "rightPane")
svalue(idp$gui$gall)<-IDP.getSettings(idp, "centerPane")
# block Handler (only want it to fire once)
blockHandler(idp$gui$win, ID=visHandler)
})
###### init #######
# attach init event to focus handler (enables even modal dialog loading)
visHandler <- addHandlerFocus(idp$gui$win, handler=function(...) {
# initiate screen (load whatever needs to be loaded )
# remove handler again
blockHandler(idp$gui$win, ID=visHandler)
})
dispose(load_win)
visible(idp$gui$win, TRUE)
Sys.sleep(1)
return (idp)
}
#FIXME: move all data related things to a data menu
#FIXME: move plot manipulation to plot menu
#FIXME: add menu item for copy peak table (to make shortcut work)
# get toolbar and navigation structure
IDP.getNavXML<-function() {
### menu and toolbar navigation structure
nav.xml<-'<ui>
<menubar name="menubar">
<menu name = "IDP" action="IDP">
<menuitem action="SaveToWorkspace" />
<menuitem action="Help"/>
<menuitem action="Quit" />
</menu>
<menu name ="FileMenu" action ="File">
<menuitem action ="OpenFile" />
<menuitem action ="CloseFile" />
<menuitem action ="CloseAll" />
</menu>
<menu name="View" action="View">
<menuitem action="ZoomBack"/>
<menuitem action="ZoomFull"/>
<menuitem action="ZoomIn"/>
<menuitem action="ZoomOut"/>
<menuitem action="BestFit"/>
<menuitem action="MoveIntervalB"/>
<menuitem action="MoveIntervalF"/>
<menuitem action="SetAxes"/>
<separator/>
<menuitem action="FullScreen"/>
</menu>
<menu name="PlotMenu" action="Plot">
<menu name="XUnits" action="XUnits">
<menuitem action="XaxisSec"/>
<menuitem action="XaxisMin"/>
</menu>
<menu name="PlotOptions" action="PlotOptions">
<menuitem action="MarkRefs"/>
<menuitem action="PeakDelimsOn"/>
<menuitem action="ApexMarkerOn"/>
</menu>
<separator/>
<menu name="Mode" action="Mode">
<menuitem action ="ModeInfo"/>
<menuitem action ="ModeAdd"/>
<menuitem action ="ModeEdit"/>
<menuitem action ="ModeRefs"/>
</menu>
<menuitem action ="DeletePeak"/>
<separator/>
<menuitem action="SavePlot"/>
<menuitem action="SaveAll"/>
<separator/>
<menuitem action="PrintPlot"/>
</menu>
<menu name="DataTable" action="DataTable">
<menu name="StdsCalc" action="StdsCalc">
<menuitem action="Bracketing"/>
<menuitem action="Regression"/>
</menu>
<separator/>
<menuitem action ="CopyTable"/>
<menuitem action="TableColumns"/>
<separator/>
<menuitem action ="ExportExcel" />
<menuitem action ="ExportAll" />
</menu>
<menu name="Settings" action="Settings">
<menuitem action="EditSettings"/>
</menu>
</menubar>
<toolbar name ="toolbar">
<toolitem action = "ZoomFull"/>
<toolitem action = "ZoomIn"/>
<toolitem action = "ZoomOut"/>
<toolitem action = "BestFit"/>
<toolitem action = "MoveIntervalB"/>
<toolitem action = "MoveIntervalF"/>
<toolitem action ="SetAxes"/>
<separator/>
<toolitem action ="ModeInfo"/>
<toolitem action ="ModeAdd"/>
<toolitem action ="ModeEdit"/>
<toolitem action ="DeletePeak"/>
<toolitem action ="ModeRefs"/>
<separator/>
<toolitem action ="CopyTable"/>
<toolitem action ="Recalculate"/>
<toolitem action ="Revert"/>
</toolbar>
</ui>'
return(nav.xml)
}
sebkopf/idp documentation built on May 29, 2019, 5:52 p.m.
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##################
# Info messaging #
##################
# show an info message
# type - styling of the mssage, info, error, question, warning are the standard ones
# timer - time in seconds until message disappears automatically
# okButton - whether there is an ok button or not
IDP.showInfo<-function(idp, msg, type="question", timer=2, okButton=TRUE) {
idp$gui$infoBar$setMessageType(type)
idp$gui$infoLabel$setText(msg)
idp$gui$infoBar$show()
if (!okButton)
idp$gui$infoOkButton$hide()
else
idp$gui$infoOkButton$show()
if (!is.null(timer)) {
Sys.sleep(timer)
IDP.hideInfo(idp)
}
}
# hide info bar
IDP.hideInfo<-function(idp) {
idp$gui$infoBar$hide()
}
############
# Main GUI #
############
# launch the user interface
IDP.gui<-function(idp) {
# show a small loading window
load_win <- gwindow("Loading IDP...", width=400, height=100, visible=FALSE)
load_grp <- ggroup(horizontal=FALSE, expand=TRUE, cont=load_win)
addSpring(load_grp, expand=T)
glabel("Loading User Interface, please wait...", cont=load_grp)
addSpring(load_grp, expand=T)
visible(load_win, TRUE)
Sys.sleep(2)
# keep track of whether the DSQDP is running
IDP.running <<- TRUE
### main window
idp$gui$win <- win.init(paste("Isodat Data Processor - version", packageVersion('idp')),
width=1280, height=750, modal = idp$gui$modal, parent = idp$gui$parent)
# if (idp$gui$modal) {
# message("\nStarting IDP in modal mode (started via script).\n")
# idp$gui$win<-gbasicdialog(title=paste("Isodate File Processor - version", packageVersion('idp')), do.buttons=FALSE, visible=FALSE, parent=idp$gui$parent)
# size(idp$gui$win) <- c(1280, 750)
# } else {
# message("\nStarting IDP in window mode.\n")
# idp$gui$win<-gwindow(paste("Isodate File Processor - version", packageVersion('idp')), width=1280, height=750, visible=FALSE, parent=idp$gui$parent)
# }
# make sure to kill modal run by setting running flag back to FALSE
addHandlerDestroy(idp$gui$win, handler=function(h,...) { message("\nGoodbye!!"); IDP.running <<- FALSE })
### storing settings for easier modification
tag(idp$gui$win, "settings")<-idp$settings
### major divisions
wingrp<-ggroup(horizontal=FALSE, expand=TRUE, cont=idp$gui$win, spacing=0)
if (idp$gui$modal)
parent <- getToolkitWidget(wingrp) # get automatic toplevel gtkHBox generated by dialog
else
parent <- getToolkitWidget(wingrp)$getParent() # get automatic toplevel gtkHBox generated by gwindow
parent['border-width']<-0 # remove border
idp$gui$navgrp<-ggroup(horizontal=FALSE, cont=wingrp, spacing=0) # navigation group
# left top
glt<-ggroup(horizontal=FALSE, expand=TRUE) # left column file browser group
# left bottom
glb<-ggroup(horizontal=FALSE, expand=TRUE) # left column for file info
glbGTK<-getToolkitWidget(glb) # gtk object
glbGTK['border-width']<-5 # border with
# right top
grt<-ggroup(horizontal=TRUE, expand=TRUE) # right top
plot.grp<-ggroup(horizontal=FALSE, expand=TRUE, container=grt) # plot grp in right top
# right bottom
grb<-ggroup(horizontal=TRUE, expand=TRUE) # right bottom
tag(idp$gui$win, "tableGrp")<-ggroup(horizontal=FALSE, expand=TRUE, container=grb) # table grp in bottom right
idp$gui$gl<-gpanedgroup(glt, glb, horizontal=FALSE, expand=TRUE) # left column
idp$gui$gr<-gpanedgroup(grt, grb, horizontal=FALSE, expand=TRUE) # right column
idp$gui$gall<-gpanedgroup(idp$gui$gl, idp$gui$gr, horizontal=TRUE, container=wingrp, expand=TRUE) # total window group
### files browser
tag(idp$gui$win, "fileBrowserParentGrp")<-glt
tag(idp$gui$win, "fileBrowserGrp")<-NULL
# all the items of the file browser
fileBrowser.items <- function(path = NULL, user.data=NULL) {
topleveldir <- is.null(path)
if (topleveldir)
path <- tag(idp$gui$win, "settings")$fileDirectory # start with file directory from the settings
files <- file.info(dir(path=path, full.names=TRUE))[,c(1,2,3)] # get all files and folders
files <- data.frame(Name=dir(path=path), Dir=files[,2], stringsAsFactors=FALSE)
files <- files[union(which(files$Dir), grep("\\.cf$", files$Name)),] # only folders and .cf files
files <- files[order(-files$Dir, files$Name),] # sort by folder vs file and then name
if (topleveldir) # add "..." at the beginning (FIXME: could make sure that it's not added if at root but too lazy now)
files <- rbind(data.frame(Name="...", Dir=FALSE), files)
return(files)
}
# functions to determine which items have sub items and which icons to use
fileBrowser.hasOffspring <- function(children,user.data=NULL, ...)return(children$Dir) # which items have subdirectories
fileBrowser.icons <- function(children,user.data=NULL, ...) {
x <- rep("gtk-new", length=nrow(children))
x[which(children$Name=="...")] <- "gtk-directory" # top level folder
x[children$Dir] <- "gtk-directory" # real folders
return(x)
}
# function to remake the file tree when switching folders (FIXME: somehow looses ability for tree expansion...maybe something about how the tree is added?)
fileBrowser.gui<-function() {
if (!is.null(tag(idp$gui$win, "fileBrowserGrp")))
delete(tag(idp$gui$win, "fileBrowserParentGrp"), tag(idp$gui$win, "fileBrowserGrp"))
tag(idp$gui$win, "fileBrowserGrp") <- ggroup(expand=TRUE)
add(tag(idp$gui$win, "fileBrowserParentGrp"), tag(idp$gui$win, "fileBrowserGrp"), expand=TRUE)
tree<-gtree(fileBrowser.items, fileBrowser.hasOffspring, icon.FUN = fileBrowser.icons, container=tag(idp$gui$win, "fileBrowserGrp"), expand=TRUE, handler=function(h,...) {
if (is.null(subpath <- svalue(h$obj[]))) {
path <- IDP.getSettings(idp, "fileDirectory")
file <- svalue(h$obj)
} else {
path <- file.path(IDP.getSettings(idp, "fileDirectory"), do.call("file.path", args=as.list(subpath[-length(subpath)])))
file <- subpath[length(subpath)]
}
newpath <- file.path(path, file) # assemble new path
if (identical(file, "...")) { # except: top level directory
pathparts <- strsplit(path, .Platform$file.sep)[[1]]
newpath <- do.call("file.path", args=as.list(pathparts[-length(pathparts)]))
}
#message(newpath, "\n", path, "\n", file)
if (file.info(newpath)$isdir) { # open directory
IDP.setSettings(idp, list(fileDirectory = newpath))
fileBrowser.gui()
} else # open file
IDP.openIsodatFile(idp, path, file)
})
}
# --> file browser initialization is at the end because it needs other idp objects to be fully initialized
### file info group
idp$gui$fileInfo<-list()
idp$gui$fileInfo.nb<-gnotebook(cont = glb, expand=TRUE)
fileInfo.layout <- glayout(cont = idp$gui$fileInfo.nb, expand=TRUE, label="File Info")
fileInfo.layout[1, 1] <- "File:"
fileInfo.layout[1, 2] <- (idp$gui$fileInfo$Filename <- glabel("", cont=fileInfo.layout))
fileInfo.layout[2, 1] <- "GC:"
fileInfo.layout[2, 2] <- (idp$gui$fileInfo$GCprogram <- glabel("", cont=fileInfo.layout))
fileInfo.layout[3, 1] <- "AS:"
fileInfo.layout[3, 2] <- (idp$gui$fileInfo$ASprogram <- glabel("", cont=fileInfo.layout))
fileInfo.layout[4, 1] <- "MS:"
fileInfo.layout[4, 2] <- (idp$gui$fileInfo$MSprogram <- glabel("", cont=fileInfo.layout))
fileInfo.layout[5, 1] <- "H3:"
fileInfo.layout[5, 2] <- (idp$gui$fileInfo$H3factor <- glabel("", cont=fileInfo.layout))
### file graph
idp$gui$info.graph <- ggraphics(container=idp$gui$fileInfo.nb, label="Refs", expand=TRUE)
idp$gui$data.graph <- ggraphics(container=idp$gui$fileInfo.nb, label="Data", expand=TRUE)
### plot grp
idp$gui$pn <- pn.GUI(plot.grp, idp$gui$win, enablePlotLabel=FALSE, enableMenuButtons=FALSE, startWithTab=FALSE,
plotObjLoadHandler=function(obj) IDP.loadIsodatFileTab(idp, obj$plotinfo),
plotEventHandlers=list(
Changed = function(h,...) IDP.plotClickHandler(idp, h),
Doubleclick = function(h,...) IDP.plotDoubleClickHandler(idp, h),
Rightclick = function(h,...) IDP.plotRightClickHandler(idp, h)))
### table grp
tag(idp$gui$win, "dataTable") <- gtable(IDP.getEmptyPeakTable(idp), expand=TRUE, cont=tag(idp$gui$win, "tableGrp"))
data_table_click_handler <- function(h,...) {
if ( length(svalue(h$obj, index = TRUE)) > 0 ) IDP.plot(idp) # replot to highlight the value
}
addHandlerClicked( tag(idp$gui$win, "dataTable"), handler = data_table_click_handler)
### menu and toolbar navigation actions
nav.xml <- IDP.getNavXML()
nav.actions <-
list(## name, icon, label , accelerator , tooltip , callback
list ("IDP" , NULL , "_IDP" , NULL , NULL , NULL ) ,
list ("SaveToWorkspace" , "gtk-home" , "Save To Workspace" , "<ctrl>H" ,"Save settings to workspace" , function(...) { # include also data once ready
IDP.showInfo(idp, "Saving to workspace...", timer=1, okButton=FALSE)
IDP.save(idp)
IDP.showInfo(idp, "Isodat File Processor settings succesfully saved to workspace.", timer=2, okButton=FALSE)
} ) ,
list ("Quit", "gtk-quit", "Quit", NULL, "Quit program", function(...) { if (gconfirm("Are you sure you want to quit?")) dispose(idp$gui$win) } ),
list ("File" , NULL , "_File" , NULL , NULL , NULL ) ,
list ("OpenFile" , "gtk-open" , "Open File" , "<ctrl>O" ,"Open isodat file" , function(...) message("sorry, file selection dialog not implemented yet") ) ,
list ("CloseFile" , "gtk-close" , "Close File" , "<ctrl>W" ,"Close isodat file" , idp$gui$pn$actions$aClosePlot$handler ) ,
list ("CloseAll" , "gtk-stop" , "Close all Files" , "<ctrl><shift>W" ,"Close all isodat files" , function(...) gmessage("sorry, not implemented yet") ) ,
list ("ExportExcel" , "gtk-save-as" , "Export to Excel" , "<ctrl>X" , "Export raw data and peak table to excel" , function(...) idp.exportFileToExcel(idp) ) ,
list ("ExportAll" , "gtk-harddisk" , "Export all to Excel" , "<ctrl><shift>X" , "Export peak table for all files" , function(...) idp.exportAllPeakTablesToExcel(idp, saveAll=TRUE) ) ,
list ("Plot" , NULL , "_Chrom" , NULL , NULL , NULL ) ,
list ("SavePlot", "gtk-save-as", "Save as PDF", "<ctrl>S", "Save chromatogram as PDF", idp$gui$pn$actions$aSavePlot$handler ),
list ("SaveAll", "gtk-harddisk", "Save all", "<ctrl><shift>S", "Save all chromatograms as PDFs", idp$gui$pn$actions$aSaveAll$handler ),
list ("PrintPlot", "gtk-print", "Print", NULL, "Print chromatogram", idp$gui$pn$actions$aPrintPlot$handler ),
list ("Help" , "gtk-info" ,"Help" , NULL , NULL , function(...) gmessage("sorry, not implemented yet") ) ,
list ("View" , NULL , "_View" , NULL , NULL , NULL ) ,
list ("ZoomFull", "gtk-zoom-fit", "Unzoom", NULL, "Unzoom", function(h,...) IDP.zoomReset(idp) ),
list ("ZoomBack", "gtk-undo", "Undo Zoom", "<ctrl>Z", "Return to previous zoom", function(h,...) IDP.zoomBack(idp) ),
list ("ZoomIn", "gtk-zoom-in", "Zoom in", "<ctrl>P", "Zoom in", function(h,...) IDP.zoomIn(idp) ), # fix me, bertter short cuts?
list ("ZoomOut", "gtk-zoom-out", "Zoom out", "<ctrl>M", "Zoom out", function(h,...) IDP.zoomOut(idp) ), # fix me, better short cuts?
list ("MoveIntervalB", "gtk-go-back", "Move Left", "<ctrl><shift>Left", "Move visible window to the left", function (h,...) IDP.zoomMove(idp, -1)), # FIXME: shortcuts don't work
list ("MoveIntervalF", "gtk-go-forward", "Move Right", "<ctrl><shift>Right", "Move visible window to the right", function (h,...) IDP.zoomMove(idp, +1)), # FIXME: shortcuts don't work
list ("SetAxes", "gtk-page-setup", "Set Axes", NULL, "Set axis coordinates", function(h,...) gmessage("not implemented yet") ), # fix me, better short cuts?
list ("DataTable" , NULL , "_Data" , NULL , NULL , NULL ) ,
list ("StdsCalc" , NULL , "_Standards" , NULL , NULL , NULL ) ,
list ("Mode" , NULL , "_Mode" , NULL , NULL , NULL ) ,
list ("Settings" , NULL , "_Settings" , NULL , NULL , NULL ) ,
list ("XUnits" , NULL , "_X-axis Units" , NULL , NULL , NULL ) ,
list ("PlotOptions" , NULL , "_Plot Options" , NULL , NULL , NULL ) ,
list ("EditSettings" , "gtk-preferences" , "_Edit Settings" , NULL , NULL , function(...) {gmessage("no editable settings implemented yet, sorry")} ) ,
list ("TableColumns", "gtk-properties", "_Table Columns", NULL, "Select which peak table columns are displayed", function(...) {
dlg <- gbasicdialog(title="Select visible columns for the peak table", handler = function(h,...) {
tag(idp$gui$win, "settings")$peakTableColumns <- tbl[] # save updated peak table column settings
delete(tag(idp$gui$win, "tableGrp"), tag(idp$gui$win, "dataTable")) # delete previous table
tag(idp$gui$win, "dataTable")<-gtable(IDP.getEmptyPeakTable(idp), expand=TRUE, cont=tag(idp$gui$win, "tableGrp")) # remake current table
addHandlerClicked( tag(idp$gui$win, "dataTable"), handler = data_table_click_handler)
IDP.loadPeakTable(idp, pn.getAllInfo(idp$gui$pn)$peakTable)
})
size(dlg)<-c(500,500)
tbl <- table.toggleTable(ggroup(cont=dlg, expand=TRUE), tag(idp$gui$win, "settings")$peakTableColumns, "Show", invisibleColumns=c("Name", "Required", "IsodatCol"))
visible(dlg, set=TRUE) ## show dialog
}),
list ("DeletePeak" , "gtk-cancel" , "Delete Peak", "<ctrl>D", "Delete selected peak (<ctrl>D)" , function(...) { IDP.showInfo(idp, "Sorry, functionality not implemented yet", type="error", timer=2, okButton=FALSE) }),
list ("CopyTable" , "gtk-copy" , "Copy Table", "<ctrl>C", "Copy the peak table to the clipboard." , function(...) IDP.copyPeakTable(idp)),
list ("Recalculate" , "gtk-execute" , "Re-evaluate", "<ctrl>R", "Recalculate the isotopic composition based on the standards picked." , function(...) IDP.recalculatePeakTable(idp)),
list ("Revert" , "gtk-revert-to-saved" , "Revert All", NULL, "Discard all changes and return to original peak table from data file." , function(...) IDP.revertPeakTable(idp))
)
action_group <- gtkActionGroup ( "FileGroup" )
action_group$addActions( nav.actions )
### special actions
# full screen (toggle)
fullscreen_act<-gtkToggleAction("FullScreen", "Full Screen", "Make application full screen", stock.id="gtk-fullscreen")
gSignalConnect (fullscreen_act , "toggled" , function ( action ) {
if(fullscreen_act ['active'] )
getToolkitWidget(idp$gui$win)$fullscreen ( )
else
getToolkitWidget(idp$gui$win)$unfullscreen ( )
} )
action_group$addActionWithAccel(fullscreen_act, "<control>F")
# switch between multiple options [generic implementation]
optionsSwitch<-function(options, signals, action) {
for (name in names(options)) {
gSignalHandlerBlock(options[[name]], signals[[name]])
options[[name]]['active'] <- identical(name, action$name)
gSignalHandlerUnblock(options[[name]], signals[[name]])
}
return(action$name)
}
# switching x axis unit
xaxisActs<-list(
XaxisSec = gtkToggleAction("XaxisSec", "Seconds", "Show graph in seconds"),
XaxisMin = gtkToggleAction("XaxisMin", "Minutes", "Show graph in minuts")
)
xaxisSignals<-list()
for (name in names(xaxisActs)) {
xaxisSignals[[name]] <- gSignalConnect (xaxisActs[[name]] , "toggled", function(action) {
opt <- optionsSwitch(xaxisActs, xaxisSignals, action)
tag(idp$gui$win, "settings")$plotOptions$xUnits$value <- which(idp$settings$plotOptions$xUnits$ids == opt)
IDP.plot(idp) # replot
})
action_group$addAction(xaxisActs[[name]])
}
# plot options
MarkRefsAct = gtkToggleAction("MarkRefs", "Mark Reference Peaks", "Mark reference peaks with *")
MarkRefsAct['active']<-idp$settings$plotOptions$markRefs
gSignalConnect (MarkRefsAct, "toggled" , function ( action ) {
IDP.setSettings(idp, list("plotOptions.markRefs" = MarkRefsAct['active']))
IDP.plot(idp) # replot
} )
action_group$addAction(MarkRefsAct)
PeakDelimsOnAct = gtkToggleAction("PeakDelimsOn", "Show Peak Delimiters", "Show vertical lines to demarkate peaks")
PeakDelimsOnAct['active']<-idp$settings$plotOptions$edgeMarker$on
gSignalConnect (PeakDelimsOnAct, "toggled" , function ( action ) {
IDP.setSettings(idp, list("plotOptions.edgeMarker.on" = PeakDelimsOnAct['active']))
IDP.plot(idp) # replot
} )
action_group$addAction(PeakDelimsOnAct)
ApexMarkerOnAct = gtkToggleAction("ApexMarkerOn", "Show Apex Marker", "Show vertical lines to demarkate peak apex")
ApexMarkerOnAct['active']<-idp$settings$plotOptions$apexMarker$on
gSignalConnect (ApexMarkerOnAct, "toggled" , function ( action ) {
IDP.setSettings(idp, list("plotOptions.apexMarker.on" = ApexMarkerOnAct['active']))
IDP.plot(idp) # replot
} )
action_group$addAction(ApexMarkerOnAct)
# best fit (toggle)
idp$gui$bestfitActive<-gtkToggleAction("BestFit", "Best Fit", "Fit to tallest peak", stock.id="gtk-zoom-100")
gSignalConnect (idp$gui$bestfitActive , "toggled" , function ( action ) {
if (idp$gui$bestfitActive['active'])
IDP.zoomBest(idp)
} )
action_group$addActionWithAccel(idp$gui$bestfitActive, "<control>B")
# switch between modes
modeacts<-list(
ModeInfo = gtkToggleAction("ModeInfo", "Information", "Select peaks for information", stock.id="gtk-leave-fullscreen"),
ModeAdd = gtkToggleAction("ModeAdd", "Add Peak", "Add peaks", stock.id="gtk-add"),
ModeEdit = gtkToggleAction("ModeEdit", "Edit Peak", "Edit peaks", stock.id="gtk-redo"),
ModeRefs = gtkToggleAction("ModeRefs", "Choose Refs", "Choose isotopic reference peaks", stock.id="gtk-about"))
modeact_IDs<-list()
for (name in names(modeacts))
modeact_IDs[[name]] <- gSignalConnect (modeacts[[name]] , "toggled" , function(action) tag(idp$gui$win, "settings")$mode<-optionsSwitch(modeacts, modeact_IDs, action))
action_group$addActionWithAccel(modeacts$ModeInfo, "<control>I")
action_group$addActionWithAccel(modeacts$ModeAdd, "<control>A")
action_group$addActionWithAccel(modeacts$ModeEdit, "<control>E")
action_group$addActionWithAccel(modeacts$ModeRefs, NULL) #FIXME (control - C taken by copy peak table)
# switch between standards calc options
stdsCalcActs <- list(
Bracketing = gtkToggleAction("Bracketing", "Bracketing", "Use bracketing for standardization"),
Regression = gtkToggleAction("Regression", "Regression", "Use regression for standardization"))
stdsCalcSignals <- list()
for (name in names(stdsCalcActs)) {
stdsCalcSignals[[name]] <- gSignalConnect (stdsCalcActs[[name]] , "toggled" , function(action) {
tag(idp$gui$win, "settings")$stdsCalc <- optionsSwitch(stdsCalcActs, stdsCalcSignals, action)
})
action_group$addAction(stdsCalcActs[[name]])
}
### assemble menu
uimanager <- gtkUIManagerNew()
uimanager$insertActionGroup ( action_group , 0)
id <- uimanager$addUiFromString ( nav.xml )
gtkNavgrp <- getToolkitWidget(idp$gui$navgrp) # get navgrp gtk object
menubar <- uimanager$getWidget ( "/menubar" ) # menubar
gtkNavgrp$packStart ( menubar , FALSE )
toolbar <- uimanager$getWidget ( "/toolbar" ) # toolbar
gtkNavgrp$packStart ( toolbar , FALSE )
getToolkitWidget(idp$gui$win)$addAccelGroup ( uimanager$getAccelGroup ( ) ) # add keyboard triggers
### add information bar
idp$gui$infoBar <- gtkInfoBar (show=FALSE)
idp$gui$infoBar$setNoShowAll (TRUE)
idp$gui$infoLabel <- gtkLabel ( "Warning , Warning")
idp$gui$infoBar$setMessageType("question")
idp$gui$infoBar$getContentArea()$add(idp$gui$infoLabel)
idp$gui$infoOkButton <-idp$gui$infoBar$addButton(button.text = "gtk-ok", response.id = GtkResponseType['ok'])
gSignalConnect(idp$gui$infoBar, "response", function(infoBar, resp.id) IDP.hideInfo(idp))
getToolkitWidget(wingrp)$packStart(idp$gui$infoBar, expand=FALSE)
### initialize file browser (this late so it has access to the different objects created later)
fileBrowser.gui()
### make window visible after it's completely initialized
optionsSwitch(modeacts, modeact_IDs, list(name=idp$settings$mode)) # select right option from the start
optionsSwitch(xaxisActs, xaxisSignals, list(name=idp$settings$plotOptions$xUnits$ids[[idp$settings$plotOptions$xUnits$value]])) # select right xaxis from the start
optionsSwitch(stdsCalcActs, stdsCalcSignals, list(name=idp$settings$stdsCalc)) # select right option from the start
visHandler <- addHandlerFocus(idp$gui$win, handler=function(...) {
svalue(idp$gui$fileInfo.nb) <- 1
### starting plot and notebook positions
visible(idp$gui$info.graph) <- TRUE
plot.new()
text(0, 0, " ")
visible(idp$gui$data.graph) <- TRUE
plot.new()
text(0, 0, " ")
addHandlerChanged(idp$gui$fileInfo.nb, handler=function(h,...) {
if (h$pageno ==2) IDP.plotRefs(idp)
else if (h$pageno == 3) IDP.plotData(idp)
})
### divider positions
svalue(idp$gui$gl)<-IDP.getSettings(idp, "leftPane")
svalue(idp$gui$gr)<-IDP.getSettings(idp, "rightPane")
svalue(idp$gui$gall)<-IDP.getSettings(idp, "centerPane")
# block Handler (only want it to fire once)
blockHandler(idp$gui$win, ID=visHandler)
})
###### init #######
# attach init event to focus handler (enables even modal dialog loading)
visHandler <- addHandlerFocus(idp$gui$win, handler=function(...) {
# initiate screen (load whatever needs to be loaded )
# remove handler again
blockHandler(idp$gui$win, ID=visHandler)
})
dispose(load_win)
visible(idp$gui$win, TRUE)
Sys.sleep(1)
return (idp)
}
#FIXME: move all data related things to a data menu
#FIXME: move plot manipulation to plot menu
#FIXME: add menu item for copy peak table (to make shortcut work)
# get toolbar and navigation structure
IDP.getNavXML<-function() {
### menu and toolbar navigation structure
nav.xml<-'<ui>
<menubar name="menubar">
<menu name = "IDP" action="IDP">
<menuitem action="SaveToWorkspace" />
<menuitem action="Help"/>
<menuitem action="Quit" />
</menu>
<menu name ="FileMenu" action ="File">
<menuitem action ="OpenFile" />
<menuitem action ="CloseFile" />
<menuitem action ="CloseAll" />
</menu>
<menu name="View" action="View">
<menuitem action="ZoomBack"/>
<menuitem action="ZoomFull"/>
<menuitem action="ZoomIn"/>
<menuitem action="ZoomOut"/>
<menuitem action="BestFit"/>
<menuitem action="MoveIntervalB"/>
<menuitem action="MoveIntervalF"/>
<menuitem action="SetAxes"/>
<separator/>
<menuitem action="FullScreen"/>
</menu>
<menu name="PlotMenu" action="Plot">
<menu name="XUnits" action="XUnits">
<menuitem action="XaxisSec"/>
<menuitem action="XaxisMin"/>
</menu>
<menu name="PlotOptions" action="PlotOptions">
<menuitem action="MarkRefs"/>
<menuitem action="PeakDelimsOn"/>
<menuitem action="ApexMarkerOn"/>
</menu>
<separator/>
<menu name="Mode" action="Mode">
<menuitem action ="ModeInfo"/>
<menuitem action ="ModeAdd"/>
<menuitem action ="ModeEdit"/>
<menuitem action ="ModeRefs"/>
</menu>
<menuitem action ="DeletePeak"/>
<separator/>
<menuitem action="SavePlot"/>
<menuitem action="SaveAll"/>
<separator/>
<menuitem action="PrintPlot"/>
</menu>
<menu name="DataTable" action="DataTable">
<menu name="StdsCalc" action="StdsCalc">
<menuitem action="Bracketing"/>
<menuitem action="Regression"/>
</menu>
<separator/>
<menuitem action ="CopyTable"/>
<menuitem action="TableColumns"/>
<separator/>
<menuitem action ="ExportExcel" />
<menuitem action ="ExportAll" />
</menu>
<menu name="Settings" action="Settings">
<menuitem action="EditSettings"/>
</menu>
</menubar>
<toolbar name ="toolbar">
<toolitem action = "ZoomFull"/>
<toolitem action = "ZoomIn"/>
<toolitem action = "ZoomOut"/>
<toolitem action = "BestFit"/>
<toolitem action = "MoveIntervalB"/>
<toolitem action = "MoveIntervalF"/>
<toolitem action ="SetAxes"/>
<separator/>
<toolitem action ="ModeInfo"/>
<toolitem action ="ModeAdd"/>
<toolitem action ="ModeEdit"/>
<toolitem action ="DeletePeak"/>
<toolitem action ="ModeRefs"/>
<separator/>
<toolitem action ="CopyTable"/>
<toolitem action ="Recalculate"/>
<toolitem action ="Revert"/>
</toolbar>
</ui>'
return(nav.xml)
}
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