Thread: Using args level arguments

So I have it all done, now I just have one really bizarre issue.
You know Archie Comic's Svenson? For some reason that is the accent of my decryption software.
The output that is supposed to come out is:

\he more you eat the better you feel beans beans for every meal
the key to success is to be open to opportunity

Instead, this is what comes out:

the more vou eat the better vou feel beans beans for everv mealthe kev to success is to be open to opportunitv

a) I can't get the lines to separate so it is the format above and b) all my 'y's are being turned into 'v's.

My current code:

import java.util.*;
import java.io.*;
public class Encri {
	public static void main(String[] args) {
		try { 
			String command = args[0];
			String input = args[1];
			String output = args[2];
			File file = new File(input);
			Scanner scanner = new Scanner(file);
			String theString = scanner.nextLine();
			while (scanner.hasNextLine()) {
			       theString = theString + scanner.nextLine();
			}
			char[] charArray = theString.toCharArray();
			if (command.equalsIgnoreCase("encrypt")) {
					String keyString = args[3];
										Scanner scanned = new Scanner(keyString);
 
					int key = scanned.nextInt();
					encrypt(charArray, key, output);
			}
			if (command.equalsIgnoreCase("decrypt")) {
				String keyString = args[3];
								Scanner scanned = new Scanner(keyString);
				int key = scanned.nextInt();
				decrypt(charArray, key, output);
 
 
			}
			if (command.equalsIgnoreCase("crack")) {
				crack(charArray,output);
			}
		}
		catch (java.io.FileNotFoundException ex) {  
		System.out.println("File not found.");
		}
 
	}
	public static void encrypt(char[] array, int key, String output) {
		try {
			FileWriter filewriter = new FileWriter(new File(output));
			for (int i = 0; i < array.length; i++) {
				char space = ' ';
				if (array[i] != space) {
					int charAsNum = (int) array[i] -97;
					int decode = charAsNum + key;
					if (decode > 25) {
						decode = decode % key;
					}
					decode = decode + 97;
					char numAsChar = (char)decode;
					filewriter.write(numAsChar);
				}
				else {
					char numAsChar = ' ';
					filewriter.write(numAsChar);
				}
			}
			filewriter.close();
 
		}
		catch (java.io.IOException ex) {
			System.out.println("File not created");
			System.exit(-1);  
		}
 
	}
	public static void decrypt(char[] array, int key, String output) {
		try {
			FileWriter filewriter = new FileWriter(new File(output));
			for (int i = 0; i < array.length; i++) {
				char space = ' ';
				if (array[i] != space) {
					int charAsNum = (int) array[i] -97;
					int decode = charAsNum - key;
					if (decode < 0) {
						decode = decode + 25;
					}
					if (decode > 25) {
						decode = decode % key;
					}
					decode = decode + 97;
					char numAsChar = (char)decode;
					filewriter.write(numAsChar);
				}
				else {
					char numAsChar = ' ';
					filewriter.write(numAsChar);
				}
			}
			filewriter.close();
 
		}
		catch (java.io.IOException ex) {
			System.out.println("File not created");
			System.exit(-1);  
		}
	}
	public static void crack(char[] array, String output) {
		int[] code = new int[array.length];
		for (int i = 0; i < array.length; i++) {
			char space = ' ';
			if (array[i] != space) {
				code[i] = (int)array[i] - 97;
			}
			if (array[i] == space) {
				code[i] = 27;
			}
		}
		int[] count = new int[28];
		for (int i = 0; i <code.length; i++) {
			count[code[i]]++;
		}
		int max = count[0];
		int indexOfMax = 0;
		for (int i = 1; i < count.length; i++) {
			if (count[i] > max && count[i] < count[27]) {
				max = count[i];
				indexOfMax = i;
			}
		}	
		indexOfMax = indexOfMax + 97;
		int key = 101 - indexOfMax;
		key = key * -1;
		decrypt(array,key,output);
	}
}

I fixed the second (the y's being v's) with a minor tweak in the decrypt method, I have no idea how, in the above code, I can save the newline characters so the output will print out correctly.