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Figure out when a button is pressed in another window

I run my main window in the main method like this:
SwingUtilities.invokeLater(new Runnable() {
#Override
public void run() {
NoteSystem MainWindow = new NoteSystem();
MainWindow.initUI();
}
});
And then when a button is pressed on this form, I create a window by instantiating a class I made. I'm having trouble detecting when the second form is closed and what the textboxes/other controls contained.
What is the proper way to:
a) Fire an event in NoteSystem when the second window is closed
b) allow NoteSystem to check all the components/controls in the second window
I considered using a JOptionPane, but I'd like to create the window entirely in my own class. The idea of having the main window frozen while waiting for response from the second window works for my application though, so if I could use JOptionPane with my own class, that would be ideal.
Thanks

The best way is to use a modal dialog, a window like a JFrame, but that halts program flow in the calling code until it is no longer visible. This way, the calling code will know exactly when the dialog window has been dealt with, since its code flow will resume once again, and so often the calling code will extract information from the dialog window code at that point. A JOptionPane is one type of these, and so is a modeal JDialog (of which a JOptionPane is a sub-type). Either of these can display as complex a GUI as any that is displayed within a JFrame, so don't sell them short. You'll notice that the second parameter of most JOptionPane methods is of type Object, meaning anything can go in there, but most often you'll pass in either a String for a simple JOptionPane, or a JPanel that can be chock full of components and other nested JPanels, and in this way the JOptionPane can display the complex GUI if need be.
For examples, please see:
Passing values between JFrames
action listener to JDialog for clicked button
trouble obtaining variable info from another JFrame
How do you return a value from a java swing window closes from a button?

Exiting out of one of two JFrame exits out of both

I have two seperate JFrames but when i click the X in the topright of one, it will exit out of the other also. I have an "exit" button near the bottom to do setVisible(false), but i still have the tendency to use the x button. How would i make it so that it doesnt cancel out of the entire project?
Also, how would i make it so that the second JFrame locks out of the other JFrame untill the second JFrame is closed, like how a popup message works

Don't give your GUI two JFrames. The GUI ideally should have only one GUI. If a separate window is required, then make it a dialog such as a JDialog, and this won't happen.
Also, how would i make it so that the second JFrame locks out of the other JFrame untill the second JFrame is closed, like how a popup message works
You are perfectly describing the behavior of a modal JDialog or JOptionPane. Just use 'em.
Later we'll chat about using CardLayouts to swap views in a single GUI.
Edit, you state:
Im using Netbeans form editor to create them faster but I only see JFrame and JPanel. Can I edit them in Netbeans? I'd rather not do them through scratch Java
You've touched on another zealous belief of mine, that this is yet another reason not to use a code generator when learning a library as one can get too tied into the code generator, that it prevents one from learning the library. I strongly advise you to put aside your code-generation tool and create by hand, referring to the tutorials and API. Then later when you get more familiar with the library, sure use the tool. By the way, an answer to your direct question here is to gear your GUI's to create JPanels, and then use these JPanels where and how you want them -- in JFrames, or JDialogs, or JOptionPanes, or swapped in CardLayouts, or JTabbedPanes or nested in other JPanels,... etc...

You should be using a modal JDialog, not a second JFrame, because JDialogs provide certain functionality such as not adding another window bar to the taskbar, and automatically setting focus when the parent JFrame receives focus. Modal JDialogs prevent user input to the JFrame while it's open, useful for an "Are you sure you want to exit?" dialog, for example.
As for one JFrame exiting the other, you probably have their default close operation set to EXIT_ON_CLOSE. If you do this:
jframe.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
jframe.addWindowListener(new WindowAdapter(){
public void windowClosing(WindowEvent we){
handleUserWantsToCloseWindow();
}
});
Then you can control what happens when the user wants to close, such as popping up a "Save Changes?" modal JDialog or "Are you sure you want to quit?" modal JDialog. Note that you have to manually dispose of the JFrame if you use this method.

How can I make a Swing text area have the focus as soon as it is loaded?

I've created a simple Swing panel that, when loaded, takes up my application's entire window. It contains two JTextAreas and a handful of buttons. I want one of the text areas to have the focus when the panel loads, so that the user can immediately start typing instead of having to click on the text area first. How can I achieve this?

By default focus goes to the first component defined on the window.
If this is not the component you want to have focus then you need to request focus once the window is realized.
The Dialog Focus example shows a couple of ways to do this.

See here the Documentation which contains exactlly what you are searching for (I think):
A component can also be given the
focus programmatically, such as when
its containing frame or dialog-box is
made visible. This code snippet shows
how to give a particular component the
focus every time the window gains the
focus:
//Make textField get the focus whenever frame is activated.
frame.addWindowFocusListener(new WindowAdapter() {
public void windowGainedFocus(WindowEvent e) {
textField.requestFocusInWindow();
}
});

You just need to call requestFocus method of Jcomponent class,
public void requestFocus()
On the Component that you want to focus.
And pleas make sure that you call this method after setVisible is called for its parent component.
For example:-
You have a Jframe in which you added a JTextArea, so after calling you should call in following order:-
jframe.setVisible(true);
jarea.requestFocus();

How to over ride Dialog boxes over JFrames?

I Have a java program that does sort of this:
It starts off with dialog boxes, then after user clicks OK/Cancel or X or whatever, it goes to JFrames or dialog boxes. The JFrames also have buttons like Next/Ok, etc. As the program goes on, one JFrame (lets call it "Status Bar") is always visible on the screen and never goes away (that's what I want). (I don't want to dispose it because they hold important information that the user needs to see while making choices on future dialog boxes and other JFrames).
Now my problem occurs..when the future dialog box appears, I can't click on that JFrame "Status Bar". For some reason, I have to do something on the dialog box first. Like I have to click Ok/Cancel on the dialog box, if I get another dialog box (depends where on the program), I have same issue. Until I am blessed with another JFrame, then I can click on the "Status bar" JFrame, click buttons on it and all the good things presented on that JFrame.
One solution is to convert all my remaining dialog boxes to JFrames, but that would take a lot of time since I have all sort of dialog boxes. And then linking everything together will be time consuming.
So is there a function or code that I can tell Java...to give the user the power to interact with JFrame "Status Bar" while a dialog box is presented on the screen.
I Hope I am making sense. Please ask if something is not clear. I appreciate the help.

If you're using Java 6, you can use the new modality settings.
Modality in dialogs
Depending on your GUI design, you may wish to make the dialogs Document modal as opposed to modeless(equivalent to setModal(false)). Note that this will only work if the dialogs are shown in a different root container than the Progress JFrame.
Another option is to set a modal exclusion on the JFrame you want to be always visible. This way your dialogs can still block other frames and you don't need to remember to setModal(false) everytime you add a new dialog:
progressFrame.setModalExclusionType(Dialog.ModalExclusionType.APPLICATION_EXCLUDE);

Call setModal(false) method on all dialogues so that you will be able to go to JFrame while JDialog is open.

Bad event on java panel

I have a java panel with 4 buttons. When I click on of these buttons, a new frame appears and the first is hidden with setVisibile(false).
On that new window, I have another button, but when i click it, I got the event corresponding to the fourth button of the first window. Clicking the button again does the trick, but of course this is not acceptable.
Am I missing something? I just show the frames with
nameOfTheFrame.setVisible(true);
and I have MouseListeners on every button.
The code of the last button is simply:
System.exit(0);
EDIT
Sample code:
private void btn_joinGamePressed(java.awt.event.MouseEvent evt) {
GraphicsTools.getInstance().getCreateGame().setVisible(false);
GraphicsTools.getInstance().getMainPanel().setVisible(false);
GraphicsTools.getInstance().getRegistration().setVisible(true);
}
GraphicsTools is a Singleton.
EDIT 2
Some more informations.
I noticed that on MAC OS works fine. The problem happens only on Linux and Windows.

This must be happening because of your mouse listeners. May be it is identifying the old button in your first click which is in the same location of new button (It is just my guess).
Change the mouse listeners to action listeners. For a button, it is sufficient if you have action listener.
Try this.

Try calling revalidate() on the frames as you change their viability.
Edit:
It could be something with the creation of the frames. Make sure you are calling 'pack()` on the frames.