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Java: Close Specific JFrame Window

I hope everyone is doing well.
I've built a hangman game with a swing gui and everything works well enough, HOWEVER I am trying to make a popup show up by constructing a new JFrame object when the user wins or loses with a "you lose" message or what have you. No problem, but I want a specific window to close when activating the button listener on the popup, or when the 'x' is clicked. Assume my program has 3 windows up, and I only want to close 2 of them with one click.
I tried stuff in the area of
this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
But that specific one closes all the windows. If you want to see more specific sample code, I would happy to provide it, but it didn't seem necessary for this question.
Either way, I can't figure out how to do this. Is this possible using Swing?
Thank you so much in advance. You guys are always so helpful.

How to influence to position of a new process window in Java?

I want to open an on-screen keyboard (osk or tabtip) when a Text field gets focus. This works but, in my current case, the popup keyboard always hides the Text field.
Is there any way to either influence the position of the window when it is started or to move it once it is opened?
I start the keyboard using ProcessBuilder.
cmd /C pathToExe
For my particular case it would be enough to fix it to the top-left of the screen.
(Using Java 1.6 and eclipse3 RCP, target Windows 8)

This post might help you: Can I move another program's window to the front of focus?
They are adjusting the window's Z-position (whether it is on top of other windows or not) but the Windows API they are accessing allows you to change X and Y position, too.

how to set a specific position though command line?

String cmd = "start calc.exe";
Process process = Runtime.getRuntime().exec(codeString);
I can call calculator out, but I wish to specify a accurate position like (200,300).
how can I rewrite my cmd String?
I know that java.awt.window can set a window or frame to the specific position.
Is there any method I can use to fill frame or window with my process?

There is no clean pure java solution because JDK does not provide API that can control non-java windows. So, if you want to can use JNI/JNA.
But I can suggest you a patch that will typically work.
Windows OS allows moving windows using keyboard. Try the following manually:
Win+R
type calc and press enter
press alt+space
press M
press enter
now use arrows to move the window. Press ESC to exit this mode.
All these actions can be implemented using java.awt.Robot.
So, you can run calculator and then immediately move its window where you want.
Well, this is not clear solution, but very simple one.
Expected Problems:
Alt+space is mapped to other, custom application
Other window that started together with calc overlaps it.
User will see that window is created somewhere and then quickly moved.
So, everything depends on how important all this for you. This solution is good as an exercise or demo but bad for real commercial application.

Capturing events in X11 even after the loss of focus

I am trying to develop an application which responds to multiple digital pens (IRIS Pens) so that if any of the pen writes on paper; I relay the output to a single screen. Thus making a multi-input whiteboard for myself.
In Ubuntu these pens are recognized as mouse and thus can be handled in a similar manner as mouse events are handled.
So now what I plan to do is to handle these events in C/C++ using XLib and pass these events to a Java Swing application using JNI callback. I am able to do this but when the X11 window looses focus no events are transferred to the Swing frame. I also tried to use the root window in X11 but it does not seem to work.
Any help would be really appreciated. Thanking you in advance.

How about maximizing the C/X11 window in front of the Java one, and making it transparent? You should be able to see the Java window while still focusing on the C/X11 one.
Since you are using Ubuntu, you can achieve this using the "Opacity, brightness and saturation" plugin for Compiz. It is in the compiz-plugins-main package, and you can activate it with Compiz Settings Manager (from the compizconfig-settings-manager package). When you activate the plugin, alt+wheel is bound by default to change the transparency of the focused window.

Try reading the mouse directly. I don't remember the exact location, but you should find it in something like '/dev/input/mouseX', where X is the number of your device, ranging from 0 to n-1 devices..
When you read the packet, your application should block until the mouse moves and then your read function will return a raw mouse packet which describes the delta (which is probably more useful then the screen coordinates, in your case) and the mouse button statuses.
The raw packet can be decoded as described here: http://www.computer-engineering.org/ps2mouse/

Create a modal dialog and set it to XmDIALOG_SYSTEM_MODAL (the actual name of the property depends on your toolkit: Motif, Gtk, Qt, ...). Dialogs like this block the whole display and can never loose focus.
The drawback is of course that you can't do anything else while this dialog is on the screen.
This entry in the X11 FAQ might help.

JAVA-I don't want clicking on my app make other apps lose focus

Wow, what a stupid question you might say. But is it possible? I have a mouse move event in a Jpanel and it works even when the application is not in focus, now can I have something like that for the clicking event or something similar. And most importantly I don't want other apps (even something like the main menu) to lose focus when i click on my app.
I thought of the system's event queue but i'm not sure where that would lead me to.
Thanks in advance.
[EDIT - the purpose]
I want to create an app that mimics the users interactions with the system in a later time. for example a user takes the mouse and clicks and writes and my app will mimic that in say 2 hours time. ofcourse i would need a system hook for the outer events but i wanted to avoid os-dependant code so i basically capture the screen, take it to my app,for example the user clicks on an icon in the captured picture and then for making that come to life, i translate the coordinates to the real icon and click it (with a Robot) and in this way i can capture the user's events in my own app. the problem occurs when the user clicks on the main menu or right clicks (he's doing that in my app, and my app does that to the system so my app is in between) and ofcourse the real main menu will lose focus when the user tries to click on one of it's items.
sorry for my english.

I'm still not sure I follow what you are trying to do. But the concept of an app getting focus when you click on it is fundamental to the GUI and I suspect rather difficult to get around.
I just found this:
Focusable Windows
To support palette windows and input methods, client code can prevent a Window from becoming the focused Window. By transitivity, this prevents the Window or any of its descendants from becoming the focus owner. Non-focusable Windows may still own Windows that are focusable. By default, every Frame and Dialog is focusable. Every Window which is not a Frame or Dialog, but whose nearest owning Frame or Dialog is showing on the screen, and which has at least one Component in its focus traversal cycle, is also focusable by default. To make a Window non-focusable, use Window.setFocusableWindowState(false).
In this doucment http://java.sun.com/j2se/1.5.0/docs/api/java/awt/doc-files/FocusSpec.html
That sounds like it might do what you want.