I have checked everwhere for a fix but nothing can work to make my checkbox appear. I added it to the panel and added the panel to the window. The button is appearing so it must be a problem with the checkbox. Here is my code:
import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.Point;
import java.awt.Toolkit;
import java.awt.event.KeyEvent;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JFrame;
import javax.swing.JPanel;
public class MainApplication {
    public static Toolkit tk = Toolkit.getDefaultToolkit();
    public static void main(String[] args) {
        MainApplication instance = new MainApplication();
        instance.start();
    }
    private JFrame window;
    private JPanel mainPanel;
    private JPanel contingencyPanel;
    private JButton applyButton = new JButton("Apply Changes");
    private JCheckBox autoRedLightBox = new JCheckBox("Red Light");
    private JCheckBox autoYellowLightBox = new JCheckBox("Yellow Light");
    private JCheckBox autoGreenLightBox = new JCheckBox("Green Light");
    private JCheckBox autoBlueLightBox = new JCheckBox("Blue Light");
    public void start() {
        window = new JFrame("Main Control Window");
        mainPanel = new JPanel();
        contingencyPanel = new JPanel();
        window.setSize(1280, 720);
        window.setResizable(false);
        window.setFocusable(true);
        window.setFocusTraversalKeysEnabled(true);
        int screenWidth = (int)tk.getScreenSize().getWidth();
        int screenHeight = (int)tk.getScreenSize().getHeight();
        window.setLocation((screenWidth/2)-(window.getWidth()/2), (screenHeight/2)-(window.getHeight()/2));
        window.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        mainPanel.setLayout(null);
        contingencyPanel.setLayout(null);
        applyButton.setToolTipText("Changes will be applied to the arduino.");
        applyButton.setSize(new Dimension(120, 30));
        applyButton.setLocation(new Point((1280-120)-10, (720-56)-10));
        autoRedLightBox.setSelected(true);
        autoRedLightBox.setLocation(new Point(30, 30));
        autoRedLightBox.setMnemonic(KeyEvent.VK_R);
        mainPanel.add(applyButton);
        mainPanel.add(autoRedLightBox, BorderLayout.CENTER);
        window.add(mainPanel);
        window.setVisible(true);
    }
}
Desired Outcome:

 
     
    
 
    