R/createExperiment-function.R

In antoinepari/testRRiceTravis: testRRiceTravis package to make easier the study of the genomic of rice

#' Function to create an Experiment
#' 
#' This function allows to create an Experiment object, with a name and a
#' locus list. The locus list is a .txt file, so you have to do a "read.table"
#' of your file into a variable and put this variable as the "locus" parameter
#' in the constructor. 
#'
#' @param name The name of the Experiment
#' @param locus The Table of locus 
#' @return An Experiment
#' @export
#' @rdname createExperiment-function
createExperiment <- function(name, locus){
    ## the number of databases available. To increment every time we have
    ## one more database available
    dbAvailables <- 3
    ## to check if the number the user will put is correct or not
    correctNbdb <- FALSE
    while(!correctNbdb){
        nbdb <- as.numeric(
            readline(
                prompt="How many databases do you want to experiment : "))
        if(is.numeric(nbdb) && nbdb > 0 && nbdb <= dbAvailables){
            databases <- vector(mode='list', length=nbdb)
            correctNbdb <- TRUE
        }
        else{
            message("you have not choose a correct number of databases.")
            message("please try again")
        }
    }
    ## Allows to check if the date is good or not
    correctDate <- FALSE
    while(!correctDate){
        date <- (readline(
            prompt="Enter the date of the experiment (mm/dd/yyyy) : "))
        date <- as.Date(c(date), format =  "%m/%d/%Y")
        if(!is.na(date) && 
           format(date, '%Y') > 1900 &&
           format(date, '%Y') <= format(Sys.Date(), '%Y')){
            correctDate <- TRUE
        }
        else{
            message("please write the date in the format asked.")
        }
    }
    ## We create the list which will have the genes of the databases
    genes <- vector(mode='list', length=nbdb)
    i <- 1
    while(i <= nbdb){
        databases[i] <- as.numeric(
            readline(
                prompt = paste("Enter the number",
                               "of the database you want",
                               "(example : 1 for RAPDB) :")))
        if(databases[i] > 0 && 
           databases[i] <= dbAvailables && 
           !alreadyUsedDB(databases,i)){
            callDB <- paste("callDB",databases[i],sep="")
            ##genes[[i]] <- (do.call(callDB, args = list(locus)))
            i <- i+1
        }
        else{
            if(alreadyUsedDB(databases,i)){
                message("the database is already used. Try again")
            }
            else{
                message("this number of database not exists. Try again")
                message("You can put a number between 1 and 3")
            }
            
        }
    }
    result <- new("Experiment",
                  name=name,
                  date=date,
                  databases=databases,
                  genes=genes,
                  others=list())
    return(result)
}