package core;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;

public class RReader {
	
	//Program read an R script and runs it via command line. Thus, it needs the location of Rscript.exe, the location of 
	//the specific script that should be run and the arguments that are needed for that R program
	
	public static void readRScript(String R_location, String R_programLocation, String argument) throws IOException{
		
		Runtime rt = Runtime.getRuntime();
		
		String commands = R_location + " " + R_programLocation + " " + argument;
		
		Process proc = rt.exec(commands);
		
		BufferedReader stdInput = new BufferedReader(new 
			     InputStreamReader(proc.getInputStream()));
		BufferedReader stdError = new BufferedReader(new 
			     InputStreamReader(proc.getErrorStream()));
		String tempRoutput = "";
		String s = null;
		
		while ((s = stdInput.readLine()) != null) {
			tempRoutput = tempRoutput.concat(s).concat("~");
		}
		String[] Routput = tempRoutput.split("~");
		
		for(int i = 0; i<Routput.length; i++){
		System.out.println(i + " " + Routput[i]);
		}
		System.out.println("__________________________________________________");
		System.out.println("Errors:");
		while ((s = stdError.readLine()) != null) {
			System.out.println(s);
		}	
	}
	
	
	
	public static void main(String[] args) throws IOException{
		
		
		String locationR = "C:/Program Files/R/R-3.1.2/bin/Rscript.exe";
		String locationRProgram = "C:/Users/Theo/Documents/Uni/Hiwi_Waldminghaus/Randomisierte_Oligos/Paper/Pre_Version/script.R";
		String argument = "C:/Users/Theo/Documents/Uni/Hiwi_Waldminghaus/Randomisierte_Oligos/Paper/test/h_ 50 100";

		readRScript(locationR, locationRProgram, argument);
		
	}
}