I'm pretty new to Java (currently enrolled in my first programming class), so the answer to my question could be right in front of me.

My goal is to read in a text file that reads as follows:

4563123,112211324135412
2312311,222121324135211
2312345,112211324135421
5527687,212111313124412
7867567,111111111111111

where the first set of numbers is an ID, and the second set is a set of answers to a test (of which I have the key). Once I've read in the answers I need to store them in an array (and I assume just an array, as my class has not covered ArrayLists yet). All of this data would need to be stored in one array, since I need to return it at the end of the method.

Here is the code that I have so far:

public static String[] readFile(String filename)throws IOException{
    Scanner inFile = new Scanner(filename);
    String line;
    String[] results = new String[101];
    int i = 0;
    while (inFile.hasNextLine()){
        line = inFile.nextLine();
        String[] incoming = line.split(",");
        String wid = incoming[0];
        String answer = incoming[1];
        results[i] = wid;
        results[i + 1] = answer;
        i += 2;

    }
    inFile.close();
    return results;
}

It's safe to ignore the String filename, it was passed in from the main.

Every time I run this method, I keep running into an ArrayOutOfBoundsException, mainly when I try to assign incoming[1] to answer.

I've been staring at this code longer than what is probably good for me, but it seems that I just can't wrap my head around it. Any help would be appreciated, whether that be telling me what is wrong or what I can do to improve.

Since you are using Java 7, use the new Files API and a try-with-resources statement; also, avoid copying empty lines:

final Path file = Paths.get(filename);
String line;
String[] incoming;
String[] results = new String[101];
int nrElements = 0;

try (
    final BufferedReader reader = Files.newBufferedReader(path,
        StandardCharsets.UTF_8);
) {
    while ((line = reader.readLine()) != null) {
        incoming = line.split(",");
        if (incoming.length != 2)
            continue;
        results[nrElements++] = incoming[0];
        results[nrElements++] = incoming[1];
    }
}

return Arrays.copyOfRange(results, 0, nrElements);

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