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I have a class which extends JFrame and forms the GUI of my program. I want to use the GUI for two main purposes:

  1. I want the user to be able to input values to the program.
  2. I want the GUI to display values created by my program.

Considering my class has a lot of GUI elements, the source file is already rather large and It does not seem like good practice to bundle all the program code in with the GUI code. I'm wondering what is the best way to structure my code? I believe there is an issue where requirement 1 creates a dependency from the GUI to the program code, and the second requirement does the opposite.

So, I want one class for my GUI which contains all my GUI related tasks. I then want another class for my program logic. I should then be able to call methods from the program logic class from the GUI and vice versa.

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Sounds like you are looking for a textbook MVC (Model-View-Controller) design pattern. I recommend you google "MVC Design Pattern" for summaries and use cases. That being said, you might want to put your program logic into a "Singleton" class (again, google "Singleton Design Pattern"). A properly implemented Singleton should be accessible from any other class in your code.

Consider also a third middle class which acts solely for data storage, you put values into it for storage, and you fetch values from it for work. This now creates 3 clear segments for your code, the Data (the Model), the GUI (the View), and the logic (the Controller). Voila, you've just implemented the MVC (Model-View-Controller) design pattern...

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The business logic should not depend on the GUI logic.

Have your GUI take inputs from the user. Call business logic methods with these inputs as method arguments, and use the values returned by the methods to display the result in the GUI. The GUI thus depends on the business logic, but the reverse is not true.

If the business logic must callback the GUI, it should do so via well-defined GUI-agnostic callback interfaces, or listeners. For example, you could register a ProgressListener on some business logic object, and this object would call back the progress listener. The GUI would have an implementation of the ProgressListener which would in fact update some progress bar or text area. But the business logic only depends on the interface, and not on the specific implementation.

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I'm not sure there is one "best" way to structure GUI code. As a general rule though, you should follow MVC. Your program (Model) should never directly depend on your View code. What it's allowed to do is notify the controller that the model (or parts thereof) changed, and that whichever views are currently displaying said part of the model should be updated.

Swing already provides this abstraction layer for some of its types of component, most of the classes are (somewhat confusingly) suffixed with Model. A simple example you could look at would be BoundedRangeModel. There should be only one instance of such a Model for every "unit" of data your program manages, and different views displaying this data should share this instance. Your business code manages this object, and whenever this piece of data changes, the GUI is notified using it by firing off some event listeners.

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