OneTwoThree.java

import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.Scanner;

/*
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 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
/**
 *
 * @author Clint
 */
public class OneTwoThree {

    public static void main(String[] args) throws FileNotFoundException {
        Scanner in = new Scanner(System.in);

        File file = new File("cipher_test.txt");

        in = new Scanner(file);

        String str = "";
        ArrayList stringList = new ArrayList();
        String newStr = "";

        while (in.hasNext()) {
            str = in.next();
            str = puncRemove(str);
            newStr = str.substring(0, 1);
            stringList.add(newStr);

            if (!in.hasNext()) {
                break;
            }
            str = in.next();
            str = puncRemove(str);
            while (!TwoLetters(str)) {
                str = in.next();
            }
            newStr = str.substring(1, 2);
            stringList.add(newStr);

            if (!in.hasNext()) {
                break;
            }
            str = in.next();
            str = puncRemove(str);
            while (!ThreeLetters(str)) {
                str = in.next();
            }
            newStr = str.substring(2, 3);
            stringList.add(newStr);
        }

        for (Object nothing : stringList) {

            System.out.print(nothing);
        }

    }

    public static String puncRemove(String str) {
        String newStr = str.replaceAll("[^a-zA-Z ]", "");

        return newStr;
    }

    public static boolean TwoLetters(String str) {
        if (str.length() >= 2) {
            return true;
        } else {
            return false;
        }
    }

    public static boolean ThreeLetters(String str) {
        if (str.length() >= 3) {
            return true;
        } else {
            return false;
        }
    }

}