R/cRacker.starter.R

In cRacker: R-script suite for automated processing of proteomic peptide lists

cRacker.starter <-
function(.path1 = NA){
	#.path1 <- "/Users/henno/documents/Skripte/R-Functions/cRacker1.483-function/cRacker/"
if(is.na(.path1)){
.path1 <- paste(path.package("cRacker"),"data",sep = "/")
path1 <- .path1
setwd(.path1)
}

#require("cRacker")

license.text <-  paste( "Copyright (C) <2011>  <Henrik Zauber; Max Planck Institute for Molecular Plant Physiology>
 This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

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

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


# Set cran mirror
repos <- getOption("repos")
repos["CRAN"] <- "http://mirrors.softliste.de/cran"
options(repos = repos)

### Loading required packages:
cat("Started cRacker script suite..\n")
cat("Installing/Loading Packages:\n")
check 	<- library()
check	<- check$results[,1]

if(length(grep("pcaMethods",check)) == 0){
try(source("http://www.bioconductor.org/biocLite.R"))
try(biocLite("pcaMethods"))
}

cat("Loading pcaMethods:\n")
try(library("pcaMethods"))

.packages <- c("tcltk2","gplots","bitops"
#,"igraph",
#"plotrix",
,"gtools"
,"gdata"
,"caTools"
)
for(i in 1:length(.packages)){
	temp.i <- .packages[i]
if(length(grep(temp.i,check)) == 0){
temp.error <- try(	install.packages(temp.i,repos = "http://cran.r-project.org", dependencies = FALSE)
)

}}

for(i in c(.packages,"pcaMethods")){
	print(i)
temp.i <- grep(i,library()$results)
if(length(temp.i)== 0){
	require("tcltk")
			tkmessageBox(title="Warning",message=paste("The package",i,"is not available. Please restart cRacker after you connected to the internet. Please run cRacker with administrator rights."),icon="error",type="ok")

}

}


		#library(rgl)
#plotrary("tcltk2")
cat("Loading tcltk:\n")
require("tcltk")
require("tcltk2")

tk2font.set("TkDefaultFont",settings= "-family Tahoma -size 10 -weight normal")   

### misc
show.path.mac <- function(){
input <-getwd()
try(system(paste("open ",input), intern = TRUE, ignore.stderr = TRUE))}
show.path.win <- function(){
input <-getwd()
try(system(paste("explorer ",input), intern = TRUE, ignore.stderr = TRUE))}

# read paths:
ReadAffy 		<- function(celfile.path) return(celfile.path)
print("gerg")


.import.list 	<- read.csv(paste(.path1,"/import-config",sep = ""), stringsAsFactors = FALSE)



if(length(grep("hz.matrix.creator",ls())) == 0&1==0){
	
cat("Loading cRacker functions..")
	.path1 <- print(sub("\\\\","/",.path1))
	setwd(.path1)
	wd.install <- .path1
	if(length(grep("cracker-functions",.path1)) == 0){
	setwd("./cracker-functions")
	}
	
files <- list.files()
files <- files[#c(
				grep("hz",files,fixed = TRUE)#,
				#grep("cracker",files,fixed = TRUE))
				]
if(length(files) > 0){
for(i in 1 : length(files)){
	print(files[i])
	source(files[i])
	}
}

#library("tcltk")
cat("The following functions have been loaded:\n")
print(files)
}


.path2.set 		<- hz.path.set(import.list = .import.list,path1 = .path1)




value = "yes"
.data <- NA

while(value == "yes"){

setwd(.path1)

test.time  <- system.time(hz.script.return<- hz.script(path1=.path1,path2.set = .path2.set,  import.list = .import.list,.data=.data))	
if(exists("hz.script.return")){
	.data <- hz.script.return$.data
	
}
message <- paste("The cRacker has been eaten!\nOutput has been written into:\n\n",getwd(),"\n\nDo you like to run a new session?")

require(tcltk)
value <- tkmessageBox(message =message,    icon = "question", type = "yesnocancel", default = "yes",title = "Thx for using cRacker..")
 
value <- tclvalue(value)
if(value != "yes"){



try(hz.show.path())
}

}
	
}