For example, I have a window with a preference button. I want to make it so that when user press the preference button and checks his/her appropriate options and press ok, it saves the preference, then when user presses run on the main window, it runs accordingly to preference the user changed on the preference window.
Thank you in advance.
You can use java.util.prefs package. A simple example:
// Retrieve the user preference node for the package com.mycompany
Preferences prefs = Preferences.userNodeForPackage(com.mycompany.MyClass.class);
// Preference key name
final String PREF_NAME = "name_of_preference";
// Set the value of the preference
String newValue = "a string";
prefs.put(PREF_NAME, newValue);
// Get the value of the preference;
// default value is returned if the preference does not exist
String defaultValue = "default string";
String propertyValue = prefs.get(PREF_NAME, defaultValue); // "a string"
There are many more examples at java2s.com.