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try netbeans

It's possible to be a problem with Eclipse IDE and the way of using libraries with:

This solves something I think:

package GGG;

import java.util.Scanner; // used for console input (from the keyboard)

// Declare the class
public class toothpickPuzzle {
// Fields that can...

Try this:

package LoopPb;


import java.io.*;
import java.util.*;

class AminoToken
{

I'm confuzed because of this comment:

where is the body of mainLoop?

box.setBounds(5, 10, 5 * width, 5 * height);

how to insert formated code?
I'm new.

You don't call
wrd.FileToArray();
so you don't initialize wrd.
Try:
public void PlayGame() {
try {
wrd.FileToArray();
} catch (IOException e) {
// TODO Auto-generated catch block...