Nothing
R/mqqcGUI.R
In mqqc: Quality control of LCMS derived proteomic data
Defines functions
mqqcGUI
mqqcGUI <-
function(mqpath = NULL,UseDifferentMQ = F,MSFpath = NULL){
library(tcltk)
library(tcltk2)
require("widgetTools")
.GlobalEnv$MQQCRestartNow <- "no"
.GlobalEnv$MQQCRestored <- F
fontHeading <- tkfont.create(family = "Tahoma",size=14,weight="bold")
.GlobalEnv$aborttt2 <- T
try(load(file=paste(path.package("mqqc"),"data/Param.Rdata",sep = "/")))
.GlobalEnv$Backup <- F
outputError <- F
if(exists("output")){
if(length(output) == 0){
outputError <- T
}
}
if(!exists("output")|outputError){
#loadQ <- tkmessageBox(message = "No Parameter file found. Import new Rdata container?",type = "yesno")
#if(tclvalue(loadQ) == "yes"){
if(0){
pathToRdata <- tkgetOpenFile()
try(load(tclvalue(pathToRdata)))
}else{
output <- list(
MQ = "",
MSF = "",
folder ="",
fastaFile = "",
htmloutPath = "",
DeleteFiles = 0,
cores = 1 ,
MSFcores = 1,
SpeciesTable = T,
REpar = "\\D*_\\d*_[^_]*_PLACEHOLDER_",
REmac = "^\\D*_",
REmail = "\\D*_\\d*_PLACEHOLDER_",
REtime = "_\\d{8}_",
REmisc = "[^_]*_[^_]*_[^_]*_[^_]*",
BSAID = "P02769"
)
}
}
exportRdata <- function(){
species.path<- paste(path.package("mqqc"),"data/Param.Rdata",sep = "/")
out <- tclvalue(tkgetSaveFile(initialfile = "Param.Rdata"))
if(out!=""){
file.copy(species.path,out)
}
}
# checkMQ <- list.files(paste(path.package("mqqc"),"data",sep ="/"),pattern = "MQpath",full.name = T)
# if(length(checkMQ)> 0){
# MQpath <- tclVar(readLines(checkMQ))
# }else{MQpath <- tclVar("MQ-path")}
col <- c("#FFFFFF","#426787")
col <- rev(col)
tt <- tktoplevel(bg =col[1])
# topMenu <- tkmenu(tt) # Create a menu
# tkconfigure(tt, menu = topMenu) # Add it to the 'tt' window
# themes <- tk2theme.list()
# themeMenu <- tkmenu(topMenu, tearoff = FALSE)
# if ("alt" %in% themes) tkadd(themeMenu, "command", label = "alt",
# command = function() tk2theme("alt"))
# if ("aqua" %in% themes) tkadd(themeMenu, "command", label = "aqua",
# command = function() tk2theme("aqua"))
# if ("clam" %in% themes) tkadd(themeMenu, "command", label = "clam",
# command = function() tk2theme("clam"))
# tkadd(themeMenu, "command", label = "clearlooks",
# command = function() tk2theme("clearlooks"))
# if ("classic" %in% themes) tkadd(themeMenu, "command", label = "classic",
# command = function() tk2theme("classic"))
# if ("default" %in% themes) tkadd(themeMenu, "command", label = "default",
# command = function() tk2theme("default"))
# tkadd(themeMenu, "command", label = "keramik",
# command = function() tk2theme("keramik"))
# tkadd(themeMenu, "command", label = "plastik",
# command = function() tk2theme("plastik"))
# tkadd(themeMenu, "command", label = "radiance (fonts change too)!",
# command = function() tk2theme("radiance"))
# if ("vista" %in% themes) tkadd(themeMenu, "command", label = "vista",
# command = function() tk2theme("vista"))
# if ("winnative" %in% themes) tkadd(themeMenu, "command", label = "winnative",
# command = function() tk2theme("winnative"))
# if ("xpnative" %in% themes) tkadd(themeMenu, "command", label = "xpnative",
# command = function() tk2theme("xpnative"))
# tkadd(themeMenu, "separator")
# tkadd(themeMenu, "command", label = "Quit", command = function() tkdestroy(tt))
# tkadd(topMenu, "cascade", label = "Theme", menu = themeMenu)
# tkfocus(tt)
tkwm.title(tt,paste("MQQC",packageVersion("mqqc")))
tkgrid(tk2label(tt,text = "MaxQuant Quality Control - Settings",font = fontHeading,background = col[1], foreground = col[2]),columnspan = 3)
tkwm.resizable(tt, "FALSE","FALSE")
Tabs <- c("General Settings", "Advanced")
ttb <- tkframe(tt,bg = col[2])
tt1 <- tk2frame(ttb)
nb <- tk2notebook(tt1, tabs = Tabs) # starts notebook
tkgrid(nb,columnspan = 2,padx=5,sticky = "WE",sticky = "NSWE")
tt2 <- tk2notetab(nb, Tabs[1])
tt3 <- tk2notetab(nb, Tabs[2])
ttf1 <- tk2frame(tt2)
ttf2 <- tk2frame(tt2)
ttf3 <- tk2frame(tt2)
tkLFtable <- tk2labelframe(ttf2,text = "MQQC Parameter Table")
tk2tip(ttf2,"Set here required settings for MaxQuant and Quality Control analysis.")
init <- "/home"
# MAXQUANT -----
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse <- function(init){
File <- tclvalue(tkchooseDirectory(parent = tt2,title = "MaxQuant Folder",initialdir = init))
if(File != ""){
tclvalue(MQpath) <- File
}
}
if(length(mqpath) == 0){
MQpath <- tclVar(output$MQ)
if(output$MQ != ""){init <- output$MQ}
dirFrame <- tk2labelframe(ttf1,text = "MaxQuant Folder")
browseButton <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=MQpath,justify = "right")
tkgrid(browseButton,locationField,sticky = "NSWE",padx = 1,pady = 1)
tkgrid(dirFrame,sticky = "NSWE",padx = 3,pady = c(5,3))
tk2tip(dirFrame,"Path to MaxQuant Folder.\nCurrent supported version is 1.3.0.5.\nLater version might work as well.")
}
# AnalysisFolder -------
Analysis.Folder <- tclVar(output$folder)
dirFrame <- tk2labelframe(ttf1,text = "Analysis Folder")
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse <- function(init){
File <- tclvalue(tkchooseDirectory(parent = tt2,title = "Analysis Folder",initialdir = init))
if(File != ""){
tclvalue(Analysis.Folder) <- File
}
}
browseButton <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=Analysis.Folder,justify = "left")
tkgrid(browseButton,locationField,sticky = "NSWE",padx = 1,pady = 1)
tkgrid(dirFrame, sticky = "WENS",padx = 2,pady = c(2,2))
tk2tip(dirFrame,"MQQC Main Folder. \nNew raw files, dropped here, will be analyzed by MQQC.")
# # msfragger------
# print("HUMP")
MSF <- tclVar("")
if(length(output$MSF)== 0){
output$MSF <- ""
}
if(output$MSF== ""&length(MSFpath)>0){
print("HWEUFHWIUFHIUH")
output$MSF <- MSFpath
MSF <- tclVar(MSFpath)
}
output <<- output
try(MSFpath <- tclVar(output$MSF))
if(output$MSF != ""){init <- output$MSF}
dirFrame <- tk2labelframe(ttf1,text = "MSFragger jar")
buttonRcmdr3 <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse3 <- function(init){
File <- (tk_choose.files(caption = "MSFragger jar",default = init,multi = F,filters = matrix(c(".jar",".jar"),nrow = 1)))
if(File != ""){
tclvalue(MSFpath) <- File
}
}
browseButton3 <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse3, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=MSFpath,justify = "right")
tkgrid(browseButton3,locationField,sticky = "NSWE",padx = 1,pady = 1)
tkgrid(dirFrame,sticky = "NSWE",padx = 3,pady = c(5,3))
tk2tip(dirFrame,"Path to MSFragger.jar. Requires java.")
#------
StandardFasta <- tclVar(output$fastaFile)
dirFrame <- tk2labelframe(tt2,text = "Standard Fasta")
buttonRcmdr2 <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse2 <- function(init){
File <- tclvalue(tkgetOpenFile(parent = tt2,title = "Default Fasta File",initialdir = init))
if(File != ""){
tclvalue(StandardFasta) <- File
}
}
browseButton2 <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse2, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=StandardFasta,justify = "right")
#tkgrid(browseButton2,locationField)
#tkgrid(dirFrame,padx = 5,pady = 5)
TKMisc <- tk2labelframe(ttf2,text = "Misc")
########
# other buttons
########
cb <- tk2checkbutton(TKMisc)
cbVar <- tclVar(as.numeric(output$DeleteFiles))
tkconfigure(cb,variable=cbVar)
tk2label <- tk2label(TKMisc,text = "Clean up")
tkgrid(tk2label,cb)
tk2tip(tk2label,"If checked, analysed raw files will be deleted after 24h, only MQQC results are stored.")
########
# other buttons
########
cb <- tk2checkbutton(TKMisc)
cbVar2 <- tclVar(as.numeric(output$Debug))
tkconfigure(cb,variable=cbVar2)
tk2label <- tk2label(TKMisc,text = "Debug Mode")
tkgrid(tk2label ,cb)
tk2tip(tk2label,"Display Warnings and errors in console.")
tb1.TableOrder.var <- c("system","source")
tb1.val.pep.TableOrder <- tclVar()
if(length(output$TabOrd) == 0){output$TabOrd = "source"}
tclvalue(tb1.val.pep.TableOrder) <- (output$TabOrd)
comboBox <- tk2combobox(TKMisc,values=tb1.TableOrder.var,textvariable = tb1.val.pep.TableOrder,width = 17,state = "readonly",width = 6)
tk2labelTaOr <- tk2label(TKMisc,text = "Table Sorting")
tkgrid(tk2labelTaOr,comboBox,pady = 2,sticky = "NSWE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
tk2tip(tk2labelTaOr,"Defines the date used for table sorting. System time is the time when the MQQC run was processed and source the time when the rawfile was created.")
tb1.MQFilter.var <- c("all","db","std")
tb1.val.pep.MQFilter <- tclVar()
if(length(output$MQfilter) == 0){output$MQfilter = "all"}
tclvalue(tb1.val.pep.MQFilter) <- (output$MQfilter)
comboBox <- tk2combobox(TKMisc,values=tb1.MQFilter.var,textvariable = tb1.val.pep.MQFilter,width = 17,state = "readonly",width = 6)
tk2labelMQfil <- tk2label(TKMisc,text = "ID Filter")
tkgrid(tk2labelMQfil,comboBox,pady = 2,sticky = "NSWE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
tk2tip(tk2labelMQfil,"Define Parameter IDs, that will be analyzed.\n\n\"all\" allows all IDs to be processed, including the \"generic\"search option for undefined IDs.\n\n\"db\" allows only matching IDs to be processed. The \"generic\"search option is only used with the \"default\" tag.\n\n\"std\" allows only standard IDs as defined in the GUI to be processed")
######
# cores
######
tb1.duplicates.var <- c("auto",1:200)
tb1.val.pep.duplicates <- tclVar()
tclvalue(tb1.val.pep.duplicates) <- (output$cores)
comboBox <- tk2combobox(TKMisc,values=tb1.duplicates.var,textvariable = tb1.val.pep.duplicates,width = 17,state = "readonly",width = 6)
tk2label <- tk2label(TKMisc,text = "Max Threads")
tkgrid(tk2label,comboBox,pady = 2,sticky = "NSWE")
tk2tip(tk2label,"Maximal Number of threads MQQC is allowed to use. This includes MQ and MSFragger runs.\nIf MSFragger is installed and running, the minimal number MQQC will use, is 2, even if >Max Threads< is set to 1.
\"auto\" tries to identify the maximal number of possible threads.")
# Threads MSFragger
tb1.MSFthreads.var <- c(1:200)
tb1.val.pep.MSFthreads <- tclVar()
tclvalue(tb1.val.pep.MSFthreads) <- (output$MSFcores)
comboBox <- tk2combobox(TKMisc,values=tb1.MSFthreads.var,textvariable = tb1.val.pep.MSFthreads,width = 17,state = "readonly",width = 6)
tk2label <- tk2label(TKMisc,text = "Threads MSF")
tkgrid(tk2label,comboBox,pady = 2,sticky = "NSWE")
tk2tip(tk2label,"Number of threads MSFragger is allowed to use.")
tb1.msflower <- tclVar(as.character(output$msflower))# tclVar("._.*_.*_PLACEHOLDER")
msflower <- tkentry(TKMisc,textvariable = tb1.msflower,width = 1,background = "white")
tb1.msfupper <- tclVar(as.character(output$msfupper))# tclVar("._.*_.*_PLACEHOLDER")
msfupper <- tkentry(TKMisc,textvariable = tb1.msfupper ,width = 1,background = "white")
tkgrid(tk2label(TKMisc,text="MSF Da up:"),msfupper,padx = 3,pady=1,sticky = "WE")
tkgrid(tk2label(TKMisc,text="MSF Da :"),msflower,padx = 3,pady=1,sticky = "WE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
######
# Length of Reported List per machine
######
tb1.LL.var <- c(seq(0,200,by = 10))
tb1.val.pep.LL <- tclVar()
if(length(output$ListLength) ==0){output$ListLength <- 10}
tclvalue(tb1.val.pep.LL) <- (output$ListLength)
comboBox <- tk2combobox(TKMisc,values=tb1.LL.var,textvariable = tb1.val.pep.LL,width = 17,state = "readonly",width = 6)
tk2label <- tk2label(TKMisc,text = "List length")
tkgrid(tk2label,comboBox,pady = 2,sticky = "NSWE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
tk2tip(tk2label,"Maximal number of rows reported in the html list per machine.")
####
# set fasta files
####
speciesFun <- function(){
species.path<- list.files(path.package("mqqc"),pattern = "MQQCspecies.txt$",full.name = T,recursive = T)
species <- read.csv(species.path,sep= "\t")
try(speciesTK(species))
species$Fasta <- .GlobalEnv$mqqcSpeciesSet
write.table(species,file =species.path,quote = F, row.names = F,sep = "\t")
}
speciesFunFix <- function(){
species.path<- list.files(path.package("mqqc"),pattern = "MQQCspecies.txt$",full.name = T,recursive = T)
species <- read.csv(species.path,sep = "\t")
try(species <- fix(species))
write.table(species,file =species.path,quote = F, row.names = F,sep = "\t")
print("wrote Species Table")
}
loadSpecies <- function(){
inFile <- tclvalue(tkgetOpenFile(initialfile = "MQQCspecies.txt"))
species.path<- list.files(path.package("mqqc"),pattern = "MQQCspecies.txt$",full.name = T,recursive = T)
inF <- try(readLines(inFile,n = 1))
oldF <- try(readLines(species.path ,n = 1))
tkMes <- "yes"
if(inF== oldF){
tkMes <- tclvalue(tkmessageBox(icon = "warning",message = paste("Wrong table format!\n\nHeader doesn't match. Should be:\n",oldF,"\n but is:\n",inF,"\nImport anyway?",sep = "\n"),type = "yesno"))
}
if(tkMes == "yes"){
tkMes <- tclvalue(tkmessageBox(icon = "warning",message = paste("Backup original table?",sep = "\n"),type = "yesno"))
if(tkMes == "yes"){
out <- tclvalue(tkgetSaveFile(initialfile = "MQQCspecies.txt"))
if(out !=""){
file.copy(species.path,out, overwrite = F)
}
}
file.copy(inFile, species.path, overwrite = T)
}
}
exportSpecies <- function(){
species.path<- list.files(path.package("mqqc"),pattern = "MQQCspecies.txt$",full.name = T,recursive = T)
out <- tclvalue(tkgetSaveFile(initialfile = "MQQCspecies.txt"))
if(out!=""){
file.copy(species.path,out)
}
}
ExportImportFun <- function(){
tt2 <- tktoplevel()
tt2.rb1 <- tk2radiobutton(tt2)
tt2.rb2 <- tk2radiobutton(tt2)
tt2.quant.method <- tclVar("Backup")
tkconfigure(tt2.rb1,variable=tt2.quant.method,value="Backup")
tkconfigure(tt2.rb2,variable=tt2.quant.method,value="Restore")
tkgrid(tk2label(tt2,text = "Backup"),tk2label(tt2,text = "Restore"))
tkgrid(tt2.rb1,tt2.rb2)
# Stop Go
.GlobalEnv$aborttt2 <- T
tkgrid(tkbutton(tt2,text = "GO",command = function(){.GlobalEnv$aborttt2 <- F;tkdestroy(tt2)},bg = "#009193",fg = "white"),tkbutton(tt2,text = "Cancel",command = function(){ .GlobalEnv$aborttt2 <- T; tkdestroy(tt2)},bg = "#ff7e79",fg = "white"),columnspan = 1,padx = 3,pady = 3)
tkwait.window(tt2)
if(.GlobalEnv$aborttt2){
}else{
if(tclvalue(tt2.quant.method) == "Backup"){
Control <- tkmessageBox(type = "yesno",message= "Warning, a backup requires closing of the Interface. Do you like to continue?",icon = "warning")
if(tclvalue(Control) == "yes"){
tkdestroy(tt)
#BackupRestoreSettings("b")
.GlobalEnv$MQQCRestored <- F
.GlobalEnv$MQQCRestartNow <- "yes"
.GlobalEnv$Backup <- T
tt2.quant.method <<- tt2.quant.method
Control <<- Control
}
}else{
BackupRestoreSettings("r")
tryError <- class(try(trk <- readLines(paste(path.package("mqqc"),"data/mailSettings",sep = "/"))))
print("Refining MailSettings")
try(trk1 <- tclVar(trk[1]))
try(trk2 <- tclVar(trk[2]))
try(trk3 <- tclVar(trk[3]))
try(trk4 <- tclVar(trk[4]))
.GlobalEnv$MQQCRestored <- T
.GlobalEnv$Backup <- F
.GlobalEnv$MQQCRestartNow<- tclvalue(tkmessageBox(type = "yesno",message ="MQQC GUI needs to be restarted to apply the new settings. Restart now?"))
}
}
if(.GlobalEnv$MQQCRestartNow == "yes"){
print("Destroy")
.GlobalEnv$abort <- F
tkdestroy(tt)
}
}
######
fastaSetFix <- tk2button(tkLFtable,text = "Table",command = speciesFunFix)
tk2tip(fastaSetFix,"Edit Parameter Table.\nSettings are in table format with experiment types in rows and experiment specific parameters in columns.\n \"ExperimentID\" is the label required in the raw File name to select the correct experiment type.")
fastaSet <- tk2button(tkLFtable,text = "Fasta",command = speciesFun)
tk2tip(fastaSet,"Redefine paths to required fasta files in Parameter Table.")
exportSet <- tk2button(tkLFtable,text = "Export",command = exportSpecies)
tk2tip(exportSet,"Export Parameter Table.\nUseful to modify settings in alternative table viewers.")
loadSet <- tk2button(tkLFtable,text = "Import",command = loadSpecies)
tk2tip(loadSet,"Import a tab delimited Parameter Table.\nThe Format has to be the same as in an exported table, using the \"Export\" button.")
tkgrid(fastaSetFix ,fastaSet,pady = 2,sticky = "NSWE",padx = 1)
tkgrid(exportSet,loadSet,pady = 2,sticky = "NSWE",padx = 1)
# tkgrid(tkLFtable,columnspan = 2,sticky = "NSWE",padx = 1)
tkgrid(tkLFtable,sticky = "NSWE",padx = 5,pady = 5)
tkgrid(TKMisc,sticky = "NSWE",padx = 5,pady = 5)
####
# HTML
####
HTML <- tclVar(output$htmloutPath)
dirFrame <- tk2labelframe(ttf1,text = "HTML Path")
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse <- function(init){
File <- tclvalue(tkchooseDirectory(parent = tt2,title = "HTML Folder",initialdir = init))
if(File != ""){
tclvalue(HTML) <- File
}
}
browseButton <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=HTML)
tkgrid(browseButton,locationField,sticky = "NWES",padx = 1,pady = 1)
tkgrid(dirFrame,columnspan = 2 ,sticky = "NSWE",padx = 2,pady = c(2,2))
tk2tip(dirFrame,"Folder for MQQC report in html Format.\nDisplays Information from the last 10 runs for each Machine.\nThis folder can be located on a server to provide access over Intra/Internet.")
tkgrid(ttf1,ttf2,pady = 1,padx = 1,sticky = "NSWE")
.GlobalEnv$abort <- F
#tkgrid(ttkseparator(tt2),sticky = "WE",columnspan = 2,padx = 3,pady=1)
ExImBut <- tk2button(tt1,text = "Backup/Restore all",command = ExportImportFun)
tkgrid(ExImBut, columnspan = 3)
tk2tip(ExImBut,"Backup MQQC settings or Restore from a previous safed Backup.\n Before updating to a newer Version of MQQC, it is recommended to backup the settings which are otherwise lost.")
#tkgrid(ttkseparator(tt2),sticky = "WE",columnspan = 2,padx = 3,pady=1)
##=======
# Second Tab
#========
print("hu")
tb2.Par.GE <- tclVar(as.character(output$REpar))# tclVar("._.*_.*_PLACEHOLDER")
tb2.Machine.GE <- tclVar(as.character(output$REmac))#tclVar("._.*_.*_PLACEHOLDER")
tb2.Mail.GE <- tclVar(as.character(output$REmail))#tclVar("._.*_.*_PLACEHOLDER") #.*_.*_HZ
tb2.Time.GE <-tclVar(as.character(output$REtime))# tclVar("._.*_.*_PLACEHOLDER")
tb2.Misc.GE <-tclVar(as.character(output$REmisc))# tclVar("._.*_.*_PLACEHOLDER")
RegExp <- tk2labelframe(tt3,text = "Regular Expressions")
width <- 20
tempMachine <- tkentry(RegExp,textvariable = tb2.Machine.GE,width = width,background = "white")
tempTime <- tkentry(RegExp,textvariable = tb2.Time.GE,width = width,background = "white")
tempMail <- tkentry(RegExp,textvariable = tb2.Mail.GE,width = width,background = "white")
tempPar <- tkentry(RegExp,textvariable = tb2.Par.GE,width = width,background = "white")
tempMisc <- tkentry(RegExp,textvariable = tb2.Misc.GE,width = width,background = "white")
tkgrid(tk2label(RegExp,text = "Machine *"), tempMachine,pady = 2,sticky = "W",padx = 2)
tkgrid(tk2label(RegExp,text = "Date *"), tempTime,pady = 2,sticky = "W",padx = 2)
tkgrid(tk2label(RegExp,text = "Mail *"), tempMail,pady = 2,sticky = "W",padx = 2)
tkgrid(tk2label(RegExp,text = "Parameter"), tempPar,pady = 2,sticky = "W",padx = 2)
tkgrid(tk2label(RegExp,text = "Misc *"), tempMisc,pady = 2,sticky = "W",padx = 2)
##=======
# Machine Table
#========
myRarray <- as.character(output$Machines)
tclarray <- tclArray()
for(i in 1:length(myRarray)){
tclarray[[(i-1),0]] <- myRarray[i]
}
MachineTK <- tk2labelframe(tt3,text = "Machines")
table1 <- displayInTable(tclarray,nrow=length(tclarray),ncol=0,tt = MachineTK,height = 4)
#tkgrid(RegExp,sticky = "WE",columnspan = 1)
tkgrid(RegExp,MachineTK,sticky = "NWSE",columnspan = 1,padx = 5,pady=3)
tk2tip(MachineTK,"ID(s) of used Systems.\nOptional for html output and archive.")
tk2tip(RegExp,"Regular Expressions to identify Machine ID, Time, Mail ID and Parameter ID in the raw file name. * - optional ")
StdID <- tk2labelframe(tt3,text = "Standard Parameter IDs")
StdIDlow <- tclVar(as.character(output$StdIDlow))
StdIDhigh <- tclVar(as.character(output$StdIDhigh))
StdIDlowID <- tclVar(as.character(output$BSAID))
LowIDframe <- tk2labelframe(StdID,text = "Protein Standard")
HighIDframe <- tk2labelframe(StdID,text = "Complex Sample Standard")
LowComplex <- tk2entry(LowIDframe, textvariable= StdIDlow,justify = "left",width = 10)
HighComplex <- tk2entry(HighIDframe, textvariable= StdIDhigh,justify = "left",width = 10)
LowComplexID <- tk2entry(LowIDframe, textvariable= StdIDlowID,justify = "left",width = 10)
LowID <- tk2label(LowIDframe,text = "Parameter ID")
HighID <- tk2label(HighIDframe,text = "Parameter ID")
LowIDID <- tk2label(LowIDframe,text = "Protein ID")
tkgrid(HighID, HighComplex,pady = 2,sticky = "E",padx = 2)
tkgrid(LowID, LowComplex,pady = 2,sticky = "E",padx = 2)
tkgrid(LowIDID, LowComplexID,pady = 2,sticky = "E",padx = 2)
tkgrid(HighIDframe,sticky = "E",columnspan = 2)
tkgrid(LowIDframe,sticky = "E",columnspan = 2)
tk2tip(StdID,"Parameter IDs, referred to be used as gold standard samples.\nThese IDs need to be listed in the Parameter Setting Table.")
tk2tip(HighID,"High complex reference sample, e.g. E. coli proteome.")
tk2tip(LowID,"Low complex reference sample, e.g. bovine serumalbumin")
#========
tryError <- class(try(trk <- readLines(paste(path.package("mqqc"),"data/mailSettings",sep = "/"))))
if(tryError == "try-error"){trk <- c("Username","Password","smtp.server","mail@me.mars")}
ttTRK <- tk2labelframe(tt3,text = "Mail Settings")
trkLab1 <- tk2label(ttTRK,text = "Username",justify = "left")
trkLab2 <- tk2label(ttTRK,text = "Password",justify = "left")
trkLab3 <- tk2label(ttTRK,text = "smtp.server",justify = "left")
trkLab4 <- tk2label(ttTRK,text = "email address",justify = "left")
trkLab5 <- tk2label(ttTRK,text = "port",justify = "left")
tb1.MailSecurity.var <- c("tls","ssl","plain")
tb1.val.pep.MailSecurity <- tclVar()
if(is.na(trk[6])){output$MailSecurity = "tls"}
tclvalue(tb1.val.pep.MailSecurity) <- trk[6]
comboBox <- tk2combobox(ttTRK,values=tb1.MailSecurity.var,textvariable = tb1.val.pep.MailSecurity,width = 17,state = "readonly",width = 6)
tk2labelMailSec <- tk2label(ttTRK,text = "Security")
tkgrid(tk2labelMailSec,comboBox,pady = 2,sticky = "NSWE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
tk2tip(tk2labelMailSec,"Define Parameter IDs, that will be analyzed.\n\n\"all\" allows all IDs to be processed, including the \"generic\"search option for undefined IDs.\n\n\"db\" allows only matching IDs to be processed. The \"generic\"search option is only used with the \"default\" tag.\n\n\"std\" allows only standard IDs as defined in the GUI to be processed")
tk2tip(ttTRK,"Mail Server Settings.\nRequires Perl and email account that supports SMTP and SASL for authentication.\nIt is recommended to setup a new email account for mqqc usage only.\n WARNING! Safety of password storage in mqqc cannot be warrantied!")
trk1 <- tclVar(trk[1])
trk2 <- tclVar(trk[2])
trk3 <- tclVar(trk[3])
trk4 <- tclVar(trk[4])
if(is.na(trk[5])){
trk[5] <- 587
}
trk5 <- tclVar(trk[5])
TRK1 <- tkentry(ttTRK, textvariable = trk1,background = "white",width = 10)
TRK2 <- tkentry(ttTRK, textvariable = trk2,show = "*",background = "white",width = 10)
TRK3 <- tkentry(ttTRK, textvariable = trk3,background = "white",width = 10)
TRK4 <- tkentry(ttTRK, textvariable = trk4,background = "white",width = 10)
TRK5 <- tkentry(ttTRK, textvariable = trk5,background = "white",width = 10)
tkgrid(trkLab1,TRK1,sticky = "WE",padx = 2,pady = 2)
tkgrid(trkLab2,TRK2, sticky = "W",padx = 2,pady = 2)
tkgrid(trkLab3,TRK3, sticky = "W",padx = 2,pady = 2)
tkgrid(trkLab4,TRK4, sticky = "W",padx = 2,pady = 2)
tkgrid(trkLab5,TRK5, sticky = "W",padx = 2,pady = 2)
tkgrid(StdID ,ttTRK ,sticky = "WNSE",padx = 5,pady=5)
#========================================================
#tkwm.resizable(tt2, "FALSE","FALSE")
temp <- tk2labelframe(ttf1,text = "E-Mail IDs")
#TKBexport <- tk2button(temp,text = "Mail Settings",command = function(){tkfocus(tt3))})
TKMail <- tk2button(temp,text = "@ Edit",command = fixMailList)
TKMailImport <- tk2button(temp,text = "@ import",command = MailImport)
#TKBload <- tkbutton(ttf1,text = "export Param.Rdata",command = exportRdata)
tkgrid( TKMailImport,TKMail,padx = 3,pady=1,sticky = "WE")
#tk2tip(TKBexport,"Exports set Paths.\nA complete backup is provided with Backup/Restore all function.")
tk2tip(TKMailImport,"Import a 2 Column table with User ID in first and mail in second column.")
tk2tip(TKMail,"Edit Mailinglist.")
tkgrid(temp,sticky = "NSWE",padx = 2,pady = c(2,2))
tkgrid(tt1,columnspan = 2,padx = 1,pady = 1,sticky = "NSWE")
tkgrid(ttb,columnspan = 2,padx = 10,pady = 1,sticky = "NSWE")
tkgrid(tkbutton(tt,width = 5,font = fontHeading,text = "GO",command = function(){tkdestroy(tt)},bg = "#009193",fg = "white"),tkbutton(tt,width = 5,font = fontHeading,text = "STOP",command = function(){ .GlobalEnv$abort <- T; tkdestroy(tt)},bg = "#ff7e79",fg = "white"),columnspan = 1,padx = 3,pady = 3)
#tk2theme("clearlooks")
tkwait.window(tt)
if(.GlobalEnv$abort ){stop("abort by user")}
x <- 0
Machines <- c()
out <- 1
while(!is.null(out)){
out <- tclarray[[x,0]]
x <- x+1
if(!is.null(out)){
Machines <- c(Machines,tclvalue(out))
}
}
#print(Machines)
trk <- c(tclvalue(trk1),tclvalue(trk2),tclvalue(trk3),tclvalue(trk4),tclvalue(trk5),tclvalue(tb1.val.pep.MailSecurity))
if(!.GlobalEnv$MQQCRestored){
write(trk ,paste(path.package("mqqc"),"data/mailSettings",sep = "/"))
}
rm(trk,trk1,trk2,trk3,trk4)
cores <- tclvalue(tb1.val.pep.duplicates)
if(cores == "auto"){cores <- NULL}
if(length(mqpath) != 0){
MQ <- mqpath
}else{MQ<- tclvalue(MQpath)}
output <- list(
# MQ = tclvalue(MQpath),
MQ = MQ,
MSF = tclvalue(MSFpath),
folder = tclvalue(Analysis.Folder),
fastaFile = tclvalue(StandardFasta),
htmloutPath = tclvalue(HTML),
DeleteFiles = as.logical(as.numeric(tclvalue(cbVar))),
Debug = as.logical(as.numeric(tclvalue(cbVar2))),
cores = cores ,
MSFcores = tclvalue(tb1.val.pep.MSFthreads),
SpeciesTable = T,
REpar = tclvalue(tb2.Par.GE),
REmac = tclvalue(tb2.Machine.GE),
REmail = tclvalue(tb2.Mail.GE),
REtime = tclvalue(tb2.Time.GE),
REmisc = tclvalue(tb2.Misc.GE),
Machines = Machines,
StdIDhigh = tclvalue(StdIDhigh),
StdIDlow = tclvalue(StdIDlow),
BSAID = tclvalue(StdIDlowID),
TabOrd = tclvalue(tb1.val.pep.TableOrder),
MQfilter = tclvalue(tb1.val.pep.MQFilter),
ListLength = tclvalue(tb1.val.pep.LL),
msfupper =tclvalue(tb1.msfupper),
msflower = tclvalue(tb1.msflower)
)
if(!.GlobalEnv$MQQCRestored ){
save(output,file=paste(path.package("mqqc"),"data/Param.Rdata",sep = "/"))
}
# check settings
for(i in 1:4){
tempI <- as.character(output[[i]])
tempI <- list.files(dirname(tempI),pattern= basename(tempI))
if(length(tempI) == 0){
output[[i]] <- ""
}
}
if(.GlobalEnv$aborttt2){
}else{
if(exists("Backup")){
if(Backup ){
BackupRestoreSettings("b")
.GlobalEnv$MQQCRestored <- F
.GlobalEnv$MQQCRestartNow <- "yes"
.GlobalEnv$Backup <- F
tclvalue(tt2.quant.method) <- "nothing"
}
rm("Backup")
}
}
return(output)
}
# Param <- mqqcGUI(mqpath = "HUIh")
# print(Param$MQ)
# print(Param$MSF)
# stop()
# while(.GlobalEnv$MQQCRestartNow == "yes"){
# Param <- mqqcGUI()
# }
# # print(Param)
# RESettings <- Param[grep("^RE",names(Param))]
# #save(Param, RESettings,file = "MQQCGUIsetting.Rdata")
#
# library(mqqc)
#Param <- mqqcGUI()
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Defines functions mqqcGUI
mqqcGUI <-
function(mqpath = NULL,UseDifferentMQ = F,MSFpath = NULL){
library(tcltk)
library(tcltk2)
require("widgetTools")
.GlobalEnv$MQQCRestartNow <- "no"
.GlobalEnv$MQQCRestored <- F
fontHeading <- tkfont.create(family = "Tahoma",size=14,weight="bold")
.GlobalEnv$aborttt2 <- T
try(load(file=paste(path.package("mqqc"),"data/Param.Rdata",sep = "/")))
.GlobalEnv$Backup <- F
outputError <- F
if(exists("output")){
if(length(output) == 0){
outputError <- T
}
}
if(!exists("output")|outputError){
#loadQ <- tkmessageBox(message = "No Parameter file found. Import new Rdata container?",type = "yesno")
#if(tclvalue(loadQ) == "yes"){
if(0){
pathToRdata <- tkgetOpenFile()
try(load(tclvalue(pathToRdata)))
}else{
output <- list(
MQ = "",
MSF = "",
folder ="",
fastaFile = "",
htmloutPath = "",
DeleteFiles = 0,
cores = 1 ,
MSFcores = 1,
SpeciesTable = T,
REpar = "\\D*_\\d*_[^_]*_PLACEHOLDER_",
REmac = "^\\D*_",
REmail = "\\D*_\\d*_PLACEHOLDER_",
REtime = "_\\d{8}_",
REmisc = "[^_]*_[^_]*_[^_]*_[^_]*",
BSAID = "P02769"
)
}
}
exportRdata <- function(){
species.path<- paste(path.package("mqqc"),"data/Param.Rdata",sep = "/")
out <- tclvalue(tkgetSaveFile(initialfile = "Param.Rdata"))
if(out!=""){
file.copy(species.path,out)
}
}
# checkMQ <- list.files(paste(path.package("mqqc"),"data",sep ="/"),pattern = "MQpath",full.name = T)
# if(length(checkMQ)> 0){
# MQpath <- tclVar(readLines(checkMQ))
# }else{MQpath <- tclVar("MQ-path")}
col <- c("#FFFFFF","#426787")
col <- rev(col)
tt <- tktoplevel(bg =col[1])
# topMenu <- tkmenu(tt) # Create a menu
# tkconfigure(tt, menu = topMenu) # Add it to the 'tt' window
# themes <- tk2theme.list()
# themeMenu <- tkmenu(topMenu, tearoff = FALSE)
# if ("alt" %in% themes) tkadd(themeMenu, "command", label = "alt",
# command = function() tk2theme("alt"))
# if ("aqua" %in% themes) tkadd(themeMenu, "command", label = "aqua",
# command = function() tk2theme("aqua"))
# if ("clam" %in% themes) tkadd(themeMenu, "command", label = "clam",
# command = function() tk2theme("clam"))
# tkadd(themeMenu, "command", label = "clearlooks",
# command = function() tk2theme("clearlooks"))
# if ("classic" %in% themes) tkadd(themeMenu, "command", label = "classic",
# command = function() tk2theme("classic"))
# if ("default" %in% themes) tkadd(themeMenu, "command", label = "default",
# command = function() tk2theme("default"))
# tkadd(themeMenu, "command", label = "keramik",
# command = function() tk2theme("keramik"))
# tkadd(themeMenu, "command", label = "plastik",
# command = function() tk2theme("plastik"))
# tkadd(themeMenu, "command", label = "radiance (fonts change too)!",
# command = function() tk2theme("radiance"))
# if ("vista" %in% themes) tkadd(themeMenu, "command", label = "vista",
# command = function() tk2theme("vista"))
# if ("winnative" %in% themes) tkadd(themeMenu, "command", label = "winnative",
# command = function() tk2theme("winnative"))
# if ("xpnative" %in% themes) tkadd(themeMenu, "command", label = "xpnative",
# command = function() tk2theme("xpnative"))
# tkadd(themeMenu, "separator")
# tkadd(themeMenu, "command", label = "Quit", command = function() tkdestroy(tt))
# tkadd(topMenu, "cascade", label = "Theme", menu = themeMenu)
# tkfocus(tt)
tkwm.title(tt,paste("MQQC",packageVersion("mqqc")))
tkgrid(tk2label(tt,text = "MaxQuant Quality Control - Settings",font = fontHeading,background = col[1], foreground = col[2]),columnspan = 3)
tkwm.resizable(tt, "FALSE","FALSE")
Tabs <- c("General Settings", "Advanced")
ttb <- tkframe(tt,bg = col[2])
tt1 <- tk2frame(ttb)
nb <- tk2notebook(tt1, tabs = Tabs) # starts notebook
tkgrid(nb,columnspan = 2,padx=5,sticky = "WE",sticky = "NSWE")
tt2 <- tk2notetab(nb, Tabs[1])
tt3 <- tk2notetab(nb, Tabs[2])
ttf1 <- tk2frame(tt2)
ttf2 <- tk2frame(tt2)
ttf3 <- tk2frame(tt2)
tkLFtable <- tk2labelframe(ttf2,text = "MQQC Parameter Table")
tk2tip(ttf2,"Set here required settings for MaxQuant and Quality Control analysis.")
init <- "/home"
# MAXQUANT -----
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse <- function(init){
File <- tclvalue(tkchooseDirectory(parent = tt2,title = "MaxQuant Folder",initialdir = init))
if(File != ""){
tclvalue(MQpath) <- File
}
}
if(length(mqpath) == 0){
MQpath <- tclVar(output$MQ)
if(output$MQ != ""){init <- output$MQ}
dirFrame <- tk2labelframe(ttf1,text = "MaxQuant Folder")
browseButton <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=MQpath,justify = "right")
tkgrid(browseButton,locationField,sticky = "NSWE",padx = 1,pady = 1)
tkgrid(dirFrame,sticky = "NSWE",padx = 3,pady = c(5,3))
tk2tip(dirFrame,"Path to MaxQuant Folder.\nCurrent supported version is 1.3.0.5.\nLater version might work as well.")
}
# AnalysisFolder -------
Analysis.Folder <- tclVar(output$folder)
dirFrame <- tk2labelframe(ttf1,text = "Analysis Folder")
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse <- function(init){
File <- tclvalue(tkchooseDirectory(parent = tt2,title = "Analysis Folder",initialdir = init))
if(File != ""){
tclvalue(Analysis.Folder) <- File
}
}
browseButton <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=Analysis.Folder,justify = "left")
tkgrid(browseButton,locationField,sticky = "NSWE",padx = 1,pady = 1)
tkgrid(dirFrame, sticky = "WENS",padx = 2,pady = c(2,2))
tk2tip(dirFrame,"MQQC Main Folder. \nNew raw files, dropped here, will be analyzed by MQQC.")
# # msfragger------
# print("HUMP")
MSF <- tclVar("")
if(length(output$MSF)== 0){
output$MSF <- ""
}
if(output$MSF== ""&length(MSFpath)>0){
print("HWEUFHWIUFHIUH")
output$MSF <- MSFpath
MSF <- tclVar(MSFpath)
}
output <<- output
try(MSFpath <- tclVar(output$MSF))
if(output$MSF != ""){init <- output$MSF}
dirFrame <- tk2labelframe(ttf1,text = "MSFragger jar")
buttonRcmdr3 <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse3 <- function(init){
File <- (tk_choose.files(caption = "MSFragger jar",default = init,multi = F,filters = matrix(c(".jar",".jar"),nrow = 1)))
if(File != ""){
tclvalue(MSFpath) <- File
}
}
browseButton3 <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse3, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=MSFpath,justify = "right")
tkgrid(browseButton3,locationField,sticky = "NSWE",padx = 1,pady = 1)
tkgrid(dirFrame,sticky = "NSWE",padx = 3,pady = c(5,3))
tk2tip(dirFrame,"Path to MSFragger.jar. Requires java.")
#------
StandardFasta <- tclVar(output$fastaFile)
dirFrame <- tk2labelframe(tt2,text = "Standard Fasta")
buttonRcmdr2 <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse2 <- function(init){
File <- tclvalue(tkgetOpenFile(parent = tt2,title = "Default Fasta File",initialdir = init))
if(File != ""){
tclvalue(StandardFasta) <- File
}
}
browseButton2 <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse2, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=StandardFasta,justify = "right")
#tkgrid(browseButton2,locationField)
#tkgrid(dirFrame,padx = 5,pady = 5)
TKMisc <- tk2labelframe(ttf2,text = "Misc")
########
# other buttons
########
cb <- tk2checkbutton(TKMisc)
cbVar <- tclVar(as.numeric(output$DeleteFiles))
tkconfigure(cb,variable=cbVar)
tk2label <- tk2label(TKMisc,text = "Clean up")
tkgrid(tk2label,cb)
tk2tip(tk2label,"If checked, analysed raw files will be deleted after 24h, only MQQC results are stored.")
########
# other buttons
########
cb <- tk2checkbutton(TKMisc)
cbVar2 <- tclVar(as.numeric(output$Debug))
tkconfigure(cb,variable=cbVar2)
tk2label <- tk2label(TKMisc,text = "Debug Mode")
tkgrid(tk2label ,cb)
tk2tip(tk2label,"Display Warnings and errors in console.")
tb1.TableOrder.var <- c("system","source")
tb1.val.pep.TableOrder <- tclVar()
if(length(output$TabOrd) == 0){output$TabOrd = "source"}
tclvalue(tb1.val.pep.TableOrder) <- (output$TabOrd)
comboBox <- tk2combobox(TKMisc,values=tb1.TableOrder.var,textvariable = tb1.val.pep.TableOrder,width = 17,state = "readonly",width = 6)
tk2labelTaOr <- tk2label(TKMisc,text = "Table Sorting")
tkgrid(tk2labelTaOr,comboBox,pady = 2,sticky = "NSWE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
tk2tip(tk2labelTaOr,"Defines the date used for table sorting. System time is the time when the MQQC run was processed and source the time when the rawfile was created.")
tb1.MQFilter.var <- c("all","db","std")
tb1.val.pep.MQFilter <- tclVar()
if(length(output$MQfilter) == 0){output$MQfilter = "all"}
tclvalue(tb1.val.pep.MQFilter) <- (output$MQfilter)
comboBox <- tk2combobox(TKMisc,values=tb1.MQFilter.var,textvariable = tb1.val.pep.MQFilter,width = 17,state = "readonly",width = 6)
tk2labelMQfil <- tk2label(TKMisc,text = "ID Filter")
tkgrid(tk2labelMQfil,comboBox,pady = 2,sticky = "NSWE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
tk2tip(tk2labelMQfil,"Define Parameter IDs, that will be analyzed.\n\n\"all\" allows all IDs to be processed, including the \"generic\"search option for undefined IDs.\n\n\"db\" allows only matching IDs to be processed. The \"generic\"search option is only used with the \"default\" tag.\n\n\"std\" allows only standard IDs as defined in the GUI to be processed")
######
# cores
######
tb1.duplicates.var <- c("auto",1:200)
tb1.val.pep.duplicates <- tclVar()
tclvalue(tb1.val.pep.duplicates) <- (output$cores)
comboBox <- tk2combobox(TKMisc,values=tb1.duplicates.var,textvariable = tb1.val.pep.duplicates,width = 17,state = "readonly",width = 6)
tk2label <- tk2label(TKMisc,text = "Max Threads")
tkgrid(tk2label,comboBox,pady = 2,sticky = "NSWE")
tk2tip(tk2label,"Maximal Number of threads MQQC is allowed to use. This includes MQ and MSFragger runs.\nIf MSFragger is installed and running, the minimal number MQQC will use, is 2, even if >Max Threads< is set to 1.
\"auto\" tries to identify the maximal number of possible threads.")
# Threads MSFragger
tb1.MSFthreads.var <- c(1:200)
tb1.val.pep.MSFthreads <- tclVar()
tclvalue(tb1.val.pep.MSFthreads) <- (output$MSFcores)
comboBox <- tk2combobox(TKMisc,values=tb1.MSFthreads.var,textvariable = tb1.val.pep.MSFthreads,width = 17,state = "readonly",width = 6)
tk2label <- tk2label(TKMisc,text = "Threads MSF")
tkgrid(tk2label,comboBox,pady = 2,sticky = "NSWE")
tk2tip(tk2label,"Number of threads MSFragger is allowed to use.")
tb1.msflower <- tclVar(as.character(output$msflower))# tclVar("._.*_.*_PLACEHOLDER")
msflower <- tkentry(TKMisc,textvariable = tb1.msflower,width = 1,background = "white")
tb1.msfupper <- tclVar(as.character(output$msfupper))# tclVar("._.*_.*_PLACEHOLDER")
msfupper <- tkentry(TKMisc,textvariable = tb1.msfupper ,width = 1,background = "white")
tkgrid(tk2label(TKMisc,text="MSF Da up:"),msfupper,padx = 3,pady=1,sticky = "WE")
tkgrid(tk2label(TKMisc,text="MSF Da :"),msflower,padx = 3,pady=1,sticky = "WE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
######
# Length of Reported List per machine
######
tb1.LL.var <- c(seq(0,200,by = 10))
tb1.val.pep.LL <- tclVar()
if(length(output$ListLength) ==0){output$ListLength <- 10}
tclvalue(tb1.val.pep.LL) <- (output$ListLength)
comboBox <- tk2combobox(TKMisc,values=tb1.LL.var,textvariable = tb1.val.pep.LL,width = 17,state = "readonly",width = 6)
tk2label <- tk2label(TKMisc,text = "List length")
tkgrid(tk2label,comboBox,pady = 2,sticky = "NSWE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
tk2tip(tk2label,"Maximal number of rows reported in the html list per machine.")
####
# set fasta files
####
speciesFun <- function(){
species.path<- list.files(path.package("mqqc"),pattern = "MQQCspecies.txt$",full.name = T,recursive = T)
species <- read.csv(species.path,sep= "\t")
try(speciesTK(species))
species$Fasta <- .GlobalEnv$mqqcSpeciesSet
write.table(species,file =species.path,quote = F, row.names = F,sep = "\t")
}
speciesFunFix <- function(){
species.path<- list.files(path.package("mqqc"),pattern = "MQQCspecies.txt$",full.name = T,recursive = T)
species <- read.csv(species.path,sep = "\t")
try(species <- fix(species))
write.table(species,file =species.path,quote = F, row.names = F,sep = "\t")
print("wrote Species Table")
}
loadSpecies <- function(){
inFile <- tclvalue(tkgetOpenFile(initialfile = "MQQCspecies.txt"))
species.path<- list.files(path.package("mqqc"),pattern = "MQQCspecies.txt$",full.name = T,recursive = T)
inF <- try(readLines(inFile,n = 1))
oldF <- try(readLines(species.path ,n = 1))
tkMes <- "yes"
if(inF== oldF){
tkMes <- tclvalue(tkmessageBox(icon = "warning",message = paste("Wrong table format!\n\nHeader doesn't match. Should be:\n",oldF,"\n but is:\n",inF,"\nImport anyway?",sep = "\n"),type = "yesno"))
}
if(tkMes == "yes"){
tkMes <- tclvalue(tkmessageBox(icon = "warning",message = paste("Backup original table?",sep = "\n"),type = "yesno"))
if(tkMes == "yes"){
out <- tclvalue(tkgetSaveFile(initialfile = "MQQCspecies.txt"))
if(out !=""){
file.copy(species.path,out, overwrite = F)
}
}
file.copy(inFile, species.path, overwrite = T)
}
}
exportSpecies <- function(){
species.path<- list.files(path.package("mqqc"),pattern = "MQQCspecies.txt$",full.name = T,recursive = T)
out <- tclvalue(tkgetSaveFile(initialfile = "MQQCspecies.txt"))
if(out!=""){
file.copy(species.path,out)
}
}
ExportImportFun <- function(){
tt2 <- tktoplevel()
tt2.rb1 <- tk2radiobutton(tt2)
tt2.rb2 <- tk2radiobutton(tt2)
tt2.quant.method <- tclVar("Backup")
tkconfigure(tt2.rb1,variable=tt2.quant.method,value="Backup")
tkconfigure(tt2.rb2,variable=tt2.quant.method,value="Restore")
tkgrid(tk2label(tt2,text = "Backup"),tk2label(tt2,text = "Restore"))
tkgrid(tt2.rb1,tt2.rb2)
# Stop Go
.GlobalEnv$aborttt2 <- T
tkgrid(tkbutton(tt2,text = "GO",command = function(){.GlobalEnv$aborttt2 <- F;tkdestroy(tt2)},bg = "#009193",fg = "white"),tkbutton(tt2,text = "Cancel",command = function(){ .GlobalEnv$aborttt2 <- T; tkdestroy(tt2)},bg = "#ff7e79",fg = "white"),columnspan = 1,padx = 3,pady = 3)
tkwait.window(tt2)
if(.GlobalEnv$aborttt2){
}else{
if(tclvalue(tt2.quant.method) == "Backup"){
Control <- tkmessageBox(type = "yesno",message= "Warning, a backup requires closing of the Interface. Do you like to continue?",icon = "warning")
if(tclvalue(Control) == "yes"){
tkdestroy(tt)
#BackupRestoreSettings("b")
.GlobalEnv$MQQCRestored <- F
.GlobalEnv$MQQCRestartNow <- "yes"
.GlobalEnv$Backup <- T
tt2.quant.method <<- tt2.quant.method
Control <<- Control
}
}else{
BackupRestoreSettings("r")
tryError <- class(try(trk <- readLines(paste(path.package("mqqc"),"data/mailSettings",sep = "/"))))
print("Refining MailSettings")
try(trk1 <- tclVar(trk[1]))
try(trk2 <- tclVar(trk[2]))
try(trk3 <- tclVar(trk[3]))
try(trk4 <- tclVar(trk[4]))
.GlobalEnv$MQQCRestored <- T
.GlobalEnv$Backup <- F
.GlobalEnv$MQQCRestartNow<- tclvalue(tkmessageBox(type = "yesno",message ="MQQC GUI needs to be restarted to apply the new settings. Restart now?"))
}
}
if(.GlobalEnv$MQQCRestartNow == "yes"){
print("Destroy")
.GlobalEnv$abort <- F
tkdestroy(tt)
}
}
######
fastaSetFix <- tk2button(tkLFtable,text = "Table",command = speciesFunFix)
tk2tip(fastaSetFix,"Edit Parameter Table.\nSettings are in table format with experiment types in rows and experiment specific parameters in columns.\n \"ExperimentID\" is the label required in the raw File name to select the correct experiment type.")
fastaSet <- tk2button(tkLFtable,text = "Fasta",command = speciesFun)
tk2tip(fastaSet,"Redefine paths to required fasta files in Parameter Table.")
exportSet <- tk2button(tkLFtable,text = "Export",command = exportSpecies)
tk2tip(exportSet,"Export Parameter Table.\nUseful to modify settings in alternative table viewers.")
loadSet <- tk2button(tkLFtable,text = "Import",command = loadSpecies)
tk2tip(loadSet,"Import a tab delimited Parameter Table.\nThe Format has to be the same as in an exported table, using the \"Export\" button.")
tkgrid(fastaSetFix ,fastaSet,pady = 2,sticky = "NSWE",padx = 1)
tkgrid(exportSet,loadSet,pady = 2,sticky = "NSWE",padx = 1)
# tkgrid(tkLFtable,columnspan = 2,sticky = "NSWE",padx = 1)
tkgrid(tkLFtable,sticky = "NSWE",padx = 5,pady = 5)
tkgrid(TKMisc,sticky = "NSWE",padx = 5,pady = 5)
####
# HTML
####
HTML <- tclVar(output$htmloutPath)
dirFrame <- tk2labelframe(ttf1,text = "HTML Path")
buttonRcmdr <- function(..., borderwidth, fg, foreground, relief) ttkbutton(...)
onBrowse <- function(init){
File <- tclvalue(tkchooseDirectory(parent = tt2,title = "HTML Folder",initialdir = init))
if(File != ""){
tclvalue(HTML) <- File
}
}
browseButton <- buttonRcmdr(dirFrame, text=gettext("Browse", domain="R-Rcmdr"), command=onBrowse, borderwidth=3)
locationField <- tk2entry(dirFrame, textvariable=HTML)
tkgrid(browseButton,locationField,sticky = "NWES",padx = 1,pady = 1)
tkgrid(dirFrame,columnspan = 2 ,sticky = "NSWE",padx = 2,pady = c(2,2))
tk2tip(dirFrame,"Folder for MQQC report in html Format.\nDisplays Information from the last 10 runs for each Machine.\nThis folder can be located on a server to provide access over Intra/Internet.")
tkgrid(ttf1,ttf2,pady = 1,padx = 1,sticky = "NSWE")
.GlobalEnv$abort <- F
#tkgrid(ttkseparator(tt2),sticky = "WE",columnspan = 2,padx = 3,pady=1)
ExImBut <- tk2button(tt1,text = "Backup/Restore all",command = ExportImportFun)
tkgrid(ExImBut, columnspan = 3)
tk2tip(ExImBut,"Backup MQQC settings or Restore from a previous safed Backup.\n Before updating to a newer Version of MQQC, it is recommended to backup the settings which are otherwise lost.")
#tkgrid(ttkseparator(tt2),sticky = "WE",columnspan = 2,padx = 3,pady=1)
##=======
# Second Tab
#========
print("hu")
tb2.Par.GE <- tclVar(as.character(output$REpar))# tclVar("._.*_.*_PLACEHOLDER")
tb2.Machine.GE <- tclVar(as.character(output$REmac))#tclVar("._.*_.*_PLACEHOLDER")
tb2.Mail.GE <- tclVar(as.character(output$REmail))#tclVar("._.*_.*_PLACEHOLDER") #.*_.*_HZ
tb2.Time.GE <-tclVar(as.character(output$REtime))# tclVar("._.*_.*_PLACEHOLDER")
tb2.Misc.GE <-tclVar(as.character(output$REmisc))# tclVar("._.*_.*_PLACEHOLDER")
RegExp <- tk2labelframe(tt3,text = "Regular Expressions")
width <- 20
tempMachine <- tkentry(RegExp,textvariable = tb2.Machine.GE,width = width,background = "white")
tempTime <- tkentry(RegExp,textvariable = tb2.Time.GE,width = width,background = "white")
tempMail <- tkentry(RegExp,textvariable = tb2.Mail.GE,width = width,background = "white")
tempPar <- tkentry(RegExp,textvariable = tb2.Par.GE,width = width,background = "white")
tempMisc <- tkentry(RegExp,textvariable = tb2.Misc.GE,width = width,background = "white")
tkgrid(tk2label(RegExp,text = "Machine *"), tempMachine,pady = 2,sticky = "W",padx = 2)
tkgrid(tk2label(RegExp,text = "Date *"), tempTime,pady = 2,sticky = "W",padx = 2)
tkgrid(tk2label(RegExp,text = "Mail *"), tempMail,pady = 2,sticky = "W",padx = 2)
tkgrid(tk2label(RegExp,text = "Parameter"), tempPar,pady = 2,sticky = "W",padx = 2)
tkgrid(tk2label(RegExp,text = "Misc *"), tempMisc,pady = 2,sticky = "W",padx = 2)
##=======
# Machine Table
#========
myRarray <- as.character(output$Machines)
tclarray <- tclArray()
for(i in 1:length(myRarray)){
tclarray[[(i-1),0]] <- myRarray[i]
}
MachineTK <- tk2labelframe(tt3,text = "Machines")
table1 <- displayInTable(tclarray,nrow=length(tclarray),ncol=0,tt = MachineTK,height = 4)
#tkgrid(RegExp,sticky = "WE",columnspan = 1)
tkgrid(RegExp,MachineTK,sticky = "NWSE",columnspan = 1,padx = 5,pady=3)
tk2tip(MachineTK,"ID(s) of used Systems.\nOptional for html output and archive.")
tk2tip(RegExp,"Regular Expressions to identify Machine ID, Time, Mail ID and Parameter ID in the raw file name. * - optional ")
StdID <- tk2labelframe(tt3,text = "Standard Parameter IDs")
StdIDlow <- tclVar(as.character(output$StdIDlow))
StdIDhigh <- tclVar(as.character(output$StdIDhigh))
StdIDlowID <- tclVar(as.character(output$BSAID))
LowIDframe <- tk2labelframe(StdID,text = "Protein Standard")
HighIDframe <- tk2labelframe(StdID,text = "Complex Sample Standard")
LowComplex <- tk2entry(LowIDframe, textvariable= StdIDlow,justify = "left",width = 10)
HighComplex <- tk2entry(HighIDframe, textvariable= StdIDhigh,justify = "left",width = 10)
LowComplexID <- tk2entry(LowIDframe, textvariable= StdIDlowID,justify = "left",width = 10)
LowID <- tk2label(LowIDframe,text = "Parameter ID")
HighID <- tk2label(HighIDframe,text = "Parameter ID")
LowIDID <- tk2label(LowIDframe,text = "Protein ID")
tkgrid(HighID, HighComplex,pady = 2,sticky = "E",padx = 2)
tkgrid(LowID, LowComplex,pady = 2,sticky = "E",padx = 2)
tkgrid(LowIDID, LowComplexID,pady = 2,sticky = "E",padx = 2)
tkgrid(HighIDframe,sticky = "E",columnspan = 2)
tkgrid(LowIDframe,sticky = "E",columnspan = 2)
tk2tip(StdID,"Parameter IDs, referred to be used as gold standard samples.\nThese IDs need to be listed in the Parameter Setting Table.")
tk2tip(HighID,"High complex reference sample, e.g. E. coli proteome.")
tk2tip(LowID,"Low complex reference sample, e.g. bovine serumalbumin")
#========
tryError <- class(try(trk <- readLines(paste(path.package("mqqc"),"data/mailSettings",sep = "/"))))
if(tryError == "try-error"){trk <- c("Username","Password","smtp.server","mail@me.mars")}
ttTRK <- tk2labelframe(tt3,text = "Mail Settings")
trkLab1 <- tk2label(ttTRK,text = "Username",justify = "left")
trkLab2 <- tk2label(ttTRK,text = "Password",justify = "left")
trkLab3 <- tk2label(ttTRK,text = "smtp.server",justify = "left")
trkLab4 <- tk2label(ttTRK,text = "email address",justify = "left")
trkLab5 <- tk2label(ttTRK,text = "port",justify = "left")
tb1.MailSecurity.var <- c("tls","ssl","plain")
tb1.val.pep.MailSecurity <- tclVar()
if(is.na(trk[6])){output$MailSecurity = "tls"}
tclvalue(tb1.val.pep.MailSecurity) <- trk[6]
comboBox <- tk2combobox(ttTRK,values=tb1.MailSecurity.var,textvariable = tb1.val.pep.MailSecurity,width = 17,state = "readonly",width = 6)
tk2labelMailSec <- tk2label(ttTRK,text = "Security")
tkgrid(tk2labelMailSec,comboBox,pady = 2,sticky = "NSWE")
#tkgrid(TKMisc,sticky = "SWNE",padx = 2)
tk2tip(tk2labelMailSec,"Define Parameter IDs, that will be analyzed.\n\n\"all\" allows all IDs to be processed, including the \"generic\"search option for undefined IDs.\n\n\"db\" allows only matching IDs to be processed. The \"generic\"search option is only used with the \"default\" tag.\n\n\"std\" allows only standard IDs as defined in the GUI to be processed")
tk2tip(ttTRK,"Mail Server Settings.\nRequires Perl and email account that supports SMTP and SASL for authentication.\nIt is recommended to setup a new email account for mqqc usage only.\n WARNING! Safety of password storage in mqqc cannot be warrantied!")
trk1 <- tclVar(trk[1])
trk2 <- tclVar(trk[2])
trk3 <- tclVar(trk[3])
trk4 <- tclVar(trk[4])
if(is.na(trk[5])){
trk[5] <- 587
}
trk5 <- tclVar(trk[5])
TRK1 <- tkentry(ttTRK, textvariable = trk1,background = "white",width = 10)
TRK2 <- tkentry(ttTRK, textvariable = trk2,show = "*",background = "white",width = 10)
TRK3 <- tkentry(ttTRK, textvariable = trk3,background = "white",width = 10)
TRK4 <- tkentry(ttTRK, textvariable = trk4,background = "white",width = 10)
TRK5 <- tkentry(ttTRK, textvariable = trk5,background = "white",width = 10)
tkgrid(trkLab1,TRK1,sticky = "WE",padx = 2,pady = 2)
tkgrid(trkLab2,TRK2, sticky = "W",padx = 2,pady = 2)
tkgrid(trkLab3,TRK3, sticky = "W",padx = 2,pady = 2)
tkgrid(trkLab4,TRK4, sticky = "W",padx = 2,pady = 2)
tkgrid(trkLab5,TRK5, sticky = "W",padx = 2,pady = 2)
tkgrid(StdID ,ttTRK ,sticky = "WNSE",padx = 5,pady=5)
#========================================================
#tkwm.resizable(tt2, "FALSE","FALSE")
temp <- tk2labelframe(ttf1,text = "E-Mail IDs")
#TKBexport <- tk2button(temp,text = "Mail Settings",command = function(){tkfocus(tt3))})
TKMail <- tk2button(temp,text = "@ Edit",command = fixMailList)
TKMailImport <- tk2button(temp,text = "@ import",command = MailImport)
#TKBload <- tkbutton(ttf1,text = "export Param.Rdata",command = exportRdata)
tkgrid( TKMailImport,TKMail,padx = 3,pady=1,sticky = "WE")
#tk2tip(TKBexport,"Exports set Paths.\nA complete backup is provided with Backup/Restore all function.")
tk2tip(TKMailImport,"Import a 2 Column table with User ID in first and mail in second column.")
tk2tip(TKMail,"Edit Mailinglist.")
tkgrid(temp,sticky = "NSWE",padx = 2,pady = c(2,2))
tkgrid(tt1,columnspan = 2,padx = 1,pady = 1,sticky = "NSWE")
tkgrid(ttb,columnspan = 2,padx = 10,pady = 1,sticky = "NSWE")
tkgrid(tkbutton(tt,width = 5,font = fontHeading,text = "GO",command = function(){tkdestroy(tt)},bg = "#009193",fg = "white"),tkbutton(tt,width = 5,font = fontHeading,text = "STOP",command = function(){ .GlobalEnv$abort <- T; tkdestroy(tt)},bg = "#ff7e79",fg = "white"),columnspan = 1,padx = 3,pady = 3)
#tk2theme("clearlooks")
tkwait.window(tt)
if(.GlobalEnv$abort ){stop("abort by user")}
x <- 0
Machines <- c()
out <- 1
while(!is.null(out)){
out <- tclarray[[x,0]]
x <- x+1
if(!is.null(out)){
Machines <- c(Machines,tclvalue(out))
}
}
#print(Machines)
trk <- c(tclvalue(trk1),tclvalue(trk2),tclvalue(trk3),tclvalue(trk4),tclvalue(trk5),tclvalue(tb1.val.pep.MailSecurity))
if(!.GlobalEnv$MQQCRestored){
write(trk ,paste(path.package("mqqc"),"data/mailSettings",sep = "/"))
}
rm(trk,trk1,trk2,trk3,trk4)
cores <- tclvalue(tb1.val.pep.duplicates)
if(cores == "auto"){cores <- NULL}
if(length(mqpath) != 0){
MQ <- mqpath
}else{MQ<- tclvalue(MQpath)}
output <- list(
# MQ = tclvalue(MQpath),
MQ = MQ,
MSF = tclvalue(MSFpath),
folder = tclvalue(Analysis.Folder),
fastaFile = tclvalue(StandardFasta),
htmloutPath = tclvalue(HTML),
DeleteFiles = as.logical(as.numeric(tclvalue(cbVar))),
Debug = as.logical(as.numeric(tclvalue(cbVar2))),
cores = cores ,
MSFcores = tclvalue(tb1.val.pep.MSFthreads),
SpeciesTable = T,
REpar = tclvalue(tb2.Par.GE),
REmac = tclvalue(tb2.Machine.GE),
REmail = tclvalue(tb2.Mail.GE),
REtime = tclvalue(tb2.Time.GE),
REmisc = tclvalue(tb2.Misc.GE),
Machines = Machines,
StdIDhigh = tclvalue(StdIDhigh),
StdIDlow = tclvalue(StdIDlow),
BSAID = tclvalue(StdIDlowID),
TabOrd = tclvalue(tb1.val.pep.TableOrder),
MQfilter = tclvalue(tb1.val.pep.MQFilter),
ListLength = tclvalue(tb1.val.pep.LL),
msfupper =tclvalue(tb1.msfupper),
msflower = tclvalue(tb1.msflower)
)
if(!.GlobalEnv$MQQCRestored ){
save(output,file=paste(path.package("mqqc"),"data/Param.Rdata",sep = "/"))
}
# check settings
for(i in 1:4){
tempI <- as.character(output[[i]])
tempI <- list.files(dirname(tempI),pattern= basename(tempI))
if(length(tempI) == 0){
output[[i]] <- ""
}
}
if(.GlobalEnv$aborttt2){
}else{
if(exists("Backup")){
if(Backup ){
BackupRestoreSettings("b")
.GlobalEnv$MQQCRestored <- F
.GlobalEnv$MQQCRestartNow <- "yes"
.GlobalEnv$Backup <- F
tclvalue(tt2.quant.method) <- "nothing"
}
rm("Backup")
}
}
return(output)
}
# Param <- mqqcGUI(mqpath = "HUIh")
# print(Param$MQ)
# print(Param$MSF)
# stop()
# while(.GlobalEnv$MQQCRestartNow == "yes"){
# Param <- mqqcGUI()
# }
# # print(Param)
# RESettings <- Param[grep("^RE",names(Param))]
# #save(Param, RESettings,file = "MQQCGUIsetting.Rdata")
#
# library(mqqc)
#Param <- mqqcGUI()
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