BufferedReader seems to only read last line of file

Question

I'm trying to write a method to take a multiline tab-delimited file and return the contents of that file as an arraylist of String arrays (each line is a String[], and each such String[] is an element of an arraylist). My problem is, I can't tell if the output is correct or not. I've printed each arraylist element and String[] element as they are saved to the arraylist, and those printings look correct. But after the arraylist is returned and I print the String[] in it, they appear to only have the contents of the very last line of the file. I'm suspecting it might be something about FileReader or BufferedReader that I don't know. Anyhoo, here's the code:

public class DataParsingTest {

    static File AAPLDailyFile = new File("./textFilesForMethodTests/dataParsingPractice2.tsv");

    public static void main(String[] args) throws FileNotFoundException, IOException {
        ArrayList<String[]> stringArrayList = fileToStringArray(AAPLDailyFile);
        System.out.println("stringArray.size() = " + stringArrayList.size());
        System.out.println(stringArrayList.get(0)[0]);

        for (int i = 0; i < stringArrayList.size(); i++) {
            for (int j = 0; j < stringArrayList.get(i).length; j++) {
                System.out.println("index of arraylist is " + i + " and element at index " + j + " of that array is " + stringArrayList.get(i)[j]);
            }
        }
    }

    public static ArrayList<String[]> fileToStringArray(File file) throws FileNotFoundException, IOException {
        ArrayList<String[]> arrayListOfStringArrays = new ArrayList<String[]>();
        FileReader fileReader = new FileReader(file);
        BufferedReader bufferedReader = new BufferedReader(fileReader);
        int nextChar = 0;
        int noOfTokens = 1; // because the first token doesn't have a tab or newline before it
        int startIndex = 0, endIndex = 0, tokenIndex = 0;
        String toRead = "";
        toRead = bufferedReader.readLine();
        for (int i = 0; i < toRead.length(); i++) {
            if (toRead.charAt(i) == '\t') {
                noOfTokens++;
            }
        }
        System.out.println("noOfTokens = " + noOfTokens);
        bufferedReader.close();
        fileReader.close();
        String[] productString = new String[noOfTokens];
        startIndex = 0;
        endIndex = 0;
        tokenIndex = 0;
        FileReader fileReader2 = new FileReader(file);
        BufferedReader bufferedReader2 = new BufferedReader(fileReader2);

        tokenIndex = 0;
        int count = 1;
        while ((toRead = bufferedReader2.readLine()) != null) { 
            System.out.println("toRead = " + toRead);
            startIndex = -1; // [L - so that the first time an array element is assigned, it's upped to 0]
            endIndex = 0;
            tokenIndex = 0;
            while (true) {  
                endIndex = toRead.indexOf("\t", startIndex + 1);  
                if (endIndex == -1) {
                    productString[tokenIndex] = toRead.substring(startIndex + 1);
                    System.out.println("tokenIndex = " + tokenIndex);
                    System.out.println("productString[" + tokenIndex + "] = " + productString[tokenIndex]);
                    tokenIndex++;
                    count++;
                    arrayListOfStringArrays.add(productString);
                    System.out.println("just added an array to the list. the first element is " + productString[0]);
                    break;
                }
                productString[tokenIndex] = toRead.substring(startIndex + 1, endIndex);
                System.out.println("tokenIndex = " + tokenIndex);
                System.out.println("productString[" + tokenIndex + "] = " + productString[tokenIndex]);
                startIndex = endIndex;
                tokenIndex++;
                count++;
            }
        }
        fileReader2.close();
        bufferedReader2.close();
        return arrayListOfStringArrays;
    }
}

The input file is:

1   2
3   4
5   6

The output is:

noOfTokens = 2
toRead = 1        2
tokenIndex = 0
productString[0] = 1
tokenIndex = 1
productString[1] = 2
just added an array to the list. the first element is 1
toRead = 3        4
tokenIndex = 0
productString[0] = 3
tokenIndex = 1
productString[1] = 4
just added an array to the list. the first element is 3
toRead = 5        6
tokenIndex = 0
productString[0] = 5
tokenIndex = 1
productString[1] = 6
just added an array to the list. the first element is 5
stringArray.size() = 3
5 // from here on up, it looks like the method works correctly
index of arraylist is 0 and element at index 0 of that array is 5
index of arraylist is 0 and element at index 1 of that array is 6
index of arraylist is 1 and element at index 0 of that array is 5
index of arraylist is 1 and element at index 1 of that array is 6
index of arraylist is 2 and element at index 0 of that array is 5
index of arraylist is 2 and element at index 1 of that array is 6 //these 6 lines only reflect the last line of the input file.

Thanks a mil!

Answer 1

That looks like too much code for me to process. Try this altered fileToStringArray method.

public static ArrayList<String[]> fileToStringArray(File file) throws FileNotFoundException, IOException {
    ArrayList<String[]> returnVal = new ArrayList<String[]>();
    // Scanner is a nifty utility for reading Files
    Scanner fIn = new Scanner(file);
    // keep reading while the Scanner has lines to process
    while (fIn.hasNextLine()) {
        // take the next line of the file, and split it up by each tab
        // and add that String[] to the list
        returnVal.add(fIn.nextLine().split("\t", -1));
    }
    return returnVal;
}

Answer 2

You're only creating a single string array, and reusing that for all lines. So your ArrayList just contains multiple references to the same object. You need to understand that when you call arrayListOfStringArrays.add(productString); that's not adding a copy of the array to the ArrayList - it's just adding a reference. (The value of productString is just a reference, not the array itself.)

Just move this:

String[] productString = new String[noOfTokens];

into the while loop, and all should be well. (In this respect, anyway. You should also be closing your file handles in finally blocks.)