R/initialize.extAffylmGUI.R

In oneChannelGUI: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

#call internally oneCHannelGUI OpenALimmaFile  .
"initialize.extAffylmGUI" <- function(){
#inserire parte di affylmGUI che ridisegna completamente la grafica
	         Try(LimmaFileName <- get("LimmaFileName",affylmGUIenvironment))
	         Try(limmaDataSetNameText <- get("limmaDataSetNameText",envir=affylmGUIenvironment))
	         Try(if(LimmaFileName=="Untitled" && limmaDataSetNameText!="Untitled") LimmaFileName <- limmaDataSetNameText) # Local assignment only
	         Try(if(.Platform$OS.type=="windows")
		             Try(tkwm.title(.affylmGUIglobals$ttMain,paste("You are now using oneChannelGUI. A add-on package extending the capabilities of affylmGUI -",gsub("/","\\\\",LimmaFileName))))
	             else
		             Try(tkwm.title(.affylmGUIglobals$ttMain,paste("You are now using oneChannelGUI. A add-on package extending the capabilities of affylmGUI -",LimmaFileName)))
	         )#end of Try

          Try(topMenu <- tkmenu(.affylmGUIglobals$ttMain))
 	       	Try(tkconfigure(.affylmGUIglobals$ttMain,menu=topMenu))
#remember to change the package!!!
	       	Try(Menus <- read.table(file.path(system.file("etc",package="oneChannelGUI"),"affylmGUI-menus.affy.txt"), as.is=TRUE))
	       	Try(
		       	for (m in 1:nrow(Menus)){
			       	Try(if(Menus[m, 1] == "menu"){
					       	assign(Menus[m, 2], tkmenu(eval(parse(text=Menus[m, 3])), tearoff=FALSE))
				       	}else if(Menus[m, 1] == "item"){
					       	if(Menus[m, 3] == "command")
						       	tkadd(eval(parse(text=Menus[m, 2])),"command", label=Menus[m, 4], command=eval(parse(text=Menus[m, 5])))
					       	else if(Menus[m, 3] == "cascade"){
						       	cascadeMenu <- eval(parse(text=Menus[m, 5]))
						       	tkadd(eval(parse(text=Menus[m, 2])),"cascade", label=Menus[m, 4], menu=cascadeMenu)
						       	if(Menus[m, 4]=="File"){
							       	Try(affylmGUIglobals <- get(".affylmGUIglobals",envir=affylmGUIenvironment))
							       	Try(menuNames <- unique(Menus[,2,drop=TRUE]))
							       	Try(numMenus <- length(menuNames))
							       	Try(menus <- list())
							       	Try(for (j in (1:numMenus))
								       	menus[[j]] <- eval(parse(text=Menus[j,2]))
							       	)#end of Try
							       	Try(names(menus) <- menuNames)
							       	Try(affylmGUIglobals$menus <- menus)
							       	Try(assign(".affylmGUIglobals",affylmGUIglobals,.GlobalEnv))
						       	}#end of if(Menus[m, 4]=="File")
					       	}else if(Menus[m, 3] == "separator"){#end of else if(Menus[m, 3] == "cascade")
						       	if(nrow(Menus)>m && Menus[m+1, 4]=="Exit"){
							       	recentFilesFileName <- system.file("etc/recent-files.txt",package="oneChannelGUI")
							       	recentFiles <- readLines(recentFilesFileName)
							       	recentFiles <- gsub("\\\\","/",recentFiles)
							       	# Remove any blank lines:
							       	blanks <- grep("^[ \t\n]*$",recentFiles)
							       	if(length(blanks)>0)
								       	recentFiles <- recentFiles[-blanks]
							       	numRecentFiles <- length(recentFiles)
							       	if(numRecentFiles>0){
								       	tkadd(eval(parse(text=Menus[m, 2])),"separator")
								       	for (i in (1:numRecentFiles)){
									       	label <- recentFiles[i]
									       	fileNameOnly <- strsplit(label,"/")[[1]]
									       	fileNameOnly <- fileNameOnly[length(fileNameOnly)]
									       	if(nchar(recentFiles[i])>60)
											       	label <- paste(".../",fileNameOnly)
									       	eval(parse(text=paste("assign(\".OpenALimmaFile_",i,"\",function() OpenALimmaFile(\"",recentFiles[i],"\"),.GlobalEnv)",sep="")))
									       	Try(
										       	if(.Platform$OS.type=="windows"){
											       	tkadd(
												       	eval(parse(text=Menus[m,2])),"command",label=paste(i,". ",gsub("/","\\\\",label),sep=""),
												       	command=eval(parse(text=paste(".OpenALimmaFile_",i,sep="")))
											       	)#end of tkadd
										       	}else{
											       	tkadd(
												       	eval(parse(text=Menus[m,2])),"command",label=paste(i,". ",label,sep=""),
												       	command=eval(parse(text=paste(".OpenALimmaFile_",i,sep="")))
											       	)#end of tkadd
										       	}#end of else/if
									       	)#end of Try
								       	}#end of for (i in (1:numRecentFiles))
							       	}#end of if(numRecentFiles>0)
						       	}#end of if(nrow(Menus)>m && Menus[m+1, 4]=="Exit")
						       	tkadd(eval(parse(text=Menus[m, 2])),"separator")
					       	}else{
						       	stop(paste("menu defintion error:", Menus[m, ], collapse=" "))
					       	}#end of else if(Menus[m, 3] == "separator")
				       	}else{
					       	stop(paste("menu defintion error:", Menus[m, ], collapse=" "))
				       	}#end of else/if(Menus[m, 1] == "item")
			       	)#end of Try(if(Menus[m, 1] == "menu") assign(Menus[m, 2], tkmenu(eval(parse(text=Menus[m, 3])), tearoff=FALSE))...)
		       	}#end of for (m in 1:nrow(Menus))
	       	)#end of Try(for (m in 1:nrow(Menus))..)

	       	Try(affylmGUIglobals <- get(".affylmGUIglobals",envir=affylmGUIenvironment))
	       	Try(affylmGUIglobals$mainMenu <- topMenu)
	       	Try(assign(".affylmGUIglobals",affylmGUIglobals,.GlobalEnv))
}