If you only need your numbers in a data structure, e.g. a flat array, then you can read the file with a Scanner and a simple loop. Scanner uses whitespace as the default delimiter, skipping multiple whitespaces.
Given List ints:
Scanner scan = new Scanner(file); // or pass an InputStream, String
while (scan.hasNext())
{
ints.add(scan.nextInt());
// ...
You'll need to handle exceptions on Scanner.nextInt.
But your proposed output data structure uses multiple arrays, one per line. You can read the file using Scanner.nextLine() to get individual lines as String. Then use String.split to split around whitespaces with a regex:
Scanner scan = new Scanner(file); // or InputStream
String line;
String[] strs;
while (scan.hasNextLine())
{
line = scan.nextLine();
// trim so that we get rid of leading whitespace, which will end
// up in strs as an empty string
strs = line.trim().split("\\s+");
// convert strs to ints
}
You could also use a second Scanner to tokenize each individual line in an inner loop. Scanner will discard any leading whitespace for you, so you can leave off the trim.