############################################################################################
# An example of an R script that illustrates how carthaGene can be setup as a server
# for mapping which is controlled from R under Unix/Linux.
# Thanks to Matthieu Falque (INRA Moulon) for this script
############################################################################################ 
#------------------------------------------------------------------------------------------------------------------------------------- 
# Initializes FIFOs  and CarthaGene
#------------------------------------------------------------------------------------------------------------------------------------- 
cg.open = function(rawName) {
     system("mkfifo CGfifoOut", intern=FALSE, ignore.stderr = FALSE, wait=TRUE, input=NULL)
     CGfifoIn <- fifo("CGfifoIn", "w+", blocking=FALSE)    # creates fifo to send commands to CG
     CGfifoOut <- fifo("CGfifoOut", "r+", blocking=FALSE)  # creates fifo to get commands from CG
     system("carthagene <CGfifoIn >CGfifoOut", intern=FALSE, ignore.stderr = FALSE, wait=FALSE, input=NULL)   # launches CG in background
     writeLines(paste("dsload", rawName), CGfifoIn)        # sends command so that CG loads dataset
     writeLines("group -u", CGfifoIn)                      # dummy command, just to know when CG has finished loading the dataset
     cg.out=readLines(CGfifoOut, n=1)
     iOk=grep("group DistThres LODThres", cg.out)
     while (length(iOk)==0) {                                                                            
	# waits for answer to "group -u" command
        cg.out=c(cg.out, readLines(CGfifoOut), n=1)
        iOk=grep("group DistThres LODThres", cg.out)
     }
     foo=readLines(CGfifoOut, n=-1)                        # empties buffer
     return(list(fifoIn=CGfifoIn, fifoOut=CGfifoOut))
}
#------------------------------------------------------------------------------------------------------------------------------------- 
# Closes CarthaGene and FIFOs
#------------------------------------------------------------------------------------------------------------------------------------- 

cg.close = function(fifoList) {    # fifoList that was returned by cg.open
     CGfifoIn=fifoList$fifoIn
     CGfifoOut=fifoList$fifoOut
     writeLines("exit", CGfifoIn)    #  sends command so CG closes
     close(CGfifoIn)                 #  closes connections
     close(CGfifoOut)
     unlink(CGfifoIn)
     unlink(CGfifoOut)
     system("rm CGfifoOut", intern=FALSE, ignore.stderr = FALSE, wait=TRUE, input=NULL) #  removes fifo files
     system("rm CGfifoIn", intern=FALSE, ignore.stderr = FALSE, wait=TRUE, input=NULL)
}