for loop in Java runs 3 times before taking next input

I’m assuming you’re on Windows, because this behavior seems about right for Windows.

When you enter a character, you do something like this:

  1. Press a
  2. Press return

Step 2 passes a line separator sequence that indicates to the input console that you have pressed enter, which tells the console that you have finished entering this line of input. So the console passes the entire line to your program.

This line separator sequence on Windows is made up of the carriage return character '\r' followed by the newline character '\n'. So your line is really "a\r\n".

What System.in.read() does is read a single byte from the input console. As the characters you input all fit into a single byte, what your program does is consumes the inputted characters one by one, so it’s something like this:

Output: Enter Character 0
> User inputs: "a\r\n" // You only entered 'a', the other two characters are from the enter key
array[0] = System.in.next(); // sets array[0] to 'a', "\r\n" are still "waiting" on the input stream

Output: Enter Character 1
> String "\r\n" is still on input, so read from those:
array[1] = System.in.next(); // sets array[1] to '\r', "\n" is still "waiting"

Output: Enter Character 2
> String "\n" is still on input, so read from that
array[2] = System.in.next(); // sets array[2] to '\n', input source is now empty

Output: Enter Character 3
> Nothing is waiting on the input stream, so program waits for user input

... and so on

What you want to do is make a Scanner, and read an entire line at once, so the only character you process is the content you entered:

Scanner scanner = new Scanner(System.in); // Creates a new scanner that reads from System.in
String line = scanner.nextLine(); // Reads an entire line from console, **not including newline breaks at the end of a line**
// use line.charAt(i) to get individual characters, or use line.toCharArray() to get the string's backing char[]

If you were to print the integer values of each of the elements in your array, you’d actually see numbers where your console outputs blank lines. These numbers are the ASCII numerical equivalents to the '\r' and '\n' characters.

Interestingly, I believe that if you were run this on a *nix system you’d only skip a single line instead of two. This is because *nix systems use just '\n' as their line separator, so you’d only have a single extra character at the end of your line.

Also, I’m not entirely sure why your console is outputting a line for both '\r' and '\n'; could be that Java breaks lines for both characters internally, while Windows does not. So you might even get different results if you were to try to run this in a Windows shell.

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