Help with filereader

[TheTurtleofDoom]

Hello I am using RoboRealm to find the hotzone, and write its x position on a file (variables). I am using the filreader to read the variables to my code(please tell my how to use spoilers) and am getting a mysterious error that only appears sometimes.
---------------------------------CODE------------------------
package recognitiotion;

import java.io.FileReader;
import java.io.IOException;

/**
*
* @author rc10545
*/
public class getCog_X {

int[] Cog_X = new int[9999];
//Creates the Cog_X array
int cogi = 0;
// controls Cog_X array

public void cog() throws IOException {

FileReader fr = new FileReader("c:/cygwin64/home/rc10545/variables");
char[] a = new char[9999999];
int i;

fr.read(a);
//updates text
String y = new String(a);
//Converts the char to one big string
String tokens[] = y.split("\r\n");
//splits the string down on every line break
i = tokens.length;
//Gets a variable for how long the tokens array is

Integer convert = Integer.valueOf(tokens[i - 2]);
// converts tokens into the convert int

Error is here between these two lines
Cog_X[cogi] = convert;
// changes the convert variable into an array

// goes to the next Cog_X array item\

}//method cog

public void positioner(int Cogx) {
System.out.println(Cogx);
int remember = 0;
//remembers wether it hass does the initial movement

if (remember == 0 && Cogx > 320) {
//goright for [five] seconds
remember++;
} else if (remember == 0) {
//goleft for [less] seconds
remember++;
}//does initial movement to bit right of the center of hotzone

if (remember == 2 && Cogx > 300 && Cogx < 330) {
System.out.println(Cogx);

} else if (remember == 1) {
remember++;
//makes sure it does not shoot while moving
}//shooter

cogi++;

}//method positioner

public void runner() throws IOException {
int Cogx;
//Positioner's Cog_X[cogi]
while (true) {
cog();

Cogx = Cog_X[cogi];
positioner(Cogx);

}//infinite while loop

}//method main

public static void main(String args[]) throws IOException {

(new getCog_X()).runner();
}

}//class
------------------------------------Code---------------------------------

--------------------------------ERROR------------------------------------
run:
Exception in thread "main" java.lang.NumberFormatException: For input string: "5
"
at java.lang.NumberFormatException.forInputString(Num berFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:492)
at java.lang.Integer.valueOf(Integer.java:582)
at recognitiotion.getCog_X.cog(getCog_X.java:32)
at recognitiotion.getCog_X.runner(getCog_X.java:73)
at recognitiotion.getCog_X.main(getCog_X.java:84)
Java Result: 1
BUILD SUCCESSFUL (total time: 0 seconds)
--------------------------------ERROR------------------------------------

[Alan Anderson]

Integer convert = Integer.valueOf(tokens[i - 2]);

What happens when y contains something that isn't parseable as an integer? For example, you might only read a partial message and end up with a null string for one of the tokens, or is less than 2 tokens long.