Develop Reference

Architecture of a multiple-windowed JavaFX 8 Application

I'm building a multi-window and multi-module simulation application, and I use JavaFX for GUI.
From what I understood, to make a JavaFX project run, you need to run Application.launch( MyApplicationSubclass.class ) and use the primary stage given in the start(Stage primaryStage) method to get started. Everything in the start method and beyond happens in a JavaFX thread.
My app is a multi-moduled application. Today, a Main class bootstraps the program and launches several modules (which are distinct Maven modules), including the one in charge of the GUI. In the beginning (when I designed the current architecture), I planned to create only one window. So, once loaded, the GUI module would make the Application.launch( MyOnlyMainWindow.class ) call, and everything would work fine.
Today, I'd like to add a console window, launched before any module, and used to "live-log" the application (by redirecting the System.out stream, between other things, into a TextFlow). But with the architecture previously described, it's impossible, because if I want ot keep the Application.launch() call in the GUI module, then I can't make it in the Console window, which is not a part of the GUI module. It would also be impossible to add another GUI module that would manage another set of window.
So I can think of two and a half ways to solve this:
Centralize, somehow, the Application.launch() call so that it is available to every class that would need it. I don't know how to do it though.
Change the Main class to heritate from javaFx Application class. But wouldn't that make me execute all my module instanciations into the JavaFX Thread? I would guess this is a bad way of doing things. Or even, if I decide to create other threads for module instanciation, those threads would have been created in the JavaFX thread.
(Use Swing for the Console Window, though it does not actually solve my problem a viable way... What if I need to create another window in another GUI module?)
What would be a viable way of creating and managing a multiple window application with JavaFX? How could I, for instance, centralize the JavaFX Application.launch() calls?
Or, in other words
Is it a good practice to decentralize the JavaFX Application implementation in a module and launch the module from the main() class, or is it better to implement it in the main() class, even if I try to make my program modular?

How do I create an interface with buttons and text?

I've tried different ways of creating different interfaces and applets. One of the main things I'm trying to do is to get these gui's to display text and show multiple buttons with different text leading to different outcomes. What I'm asking is, what code is necessary to create an applet or an interface (because I fail at telling the difference between the two) and how should I approach building and structuring that.

I recommend you use netbeans because it has an editor and is the easy way to create Applet.
https://netbeans.org/kb/docs/web/applets.html

You have three main choices I can think of, others will for sure think of something else:
Create a web server and actually serve a web site with your interface. You can code the interface yourself and communicate with your java server using ajax, you can let GWT among others do that for you. COnsider also frameworks like Struts
Create an applet which will become an embedded object in a web site. This is quickly falling out of grace, and I'd strongly discourage you from doing it, if only because of the pains of java plugins in the browser
Create an application with an interface by using AWT or Swing (which come with Java) or, and this is my personal opinion, more elegantly with SWT
It's hard to tell what will best help you without knowing more of your requirements, but if you are going web, I'd suggest you check out GWT, and if you are going desktop app, look into SWT. Also, please understand these are all well tested frameworks and my preferences are just that, preferences.

To create an interface in eclipse using java you can use swing.
In eclipse:
Create a new Java Project (File -> New -> Java Project).
Right Click on src folder and click New -> Other -> WindowBuilder -> Swing Designer -> [Application Window]/[JApplet].
Add the components that you want (buttons, textfields...).

Seems to me like your trying to graduate from console programs to GUI programs. A GUI works differently from a console program. A console program you have a bunch of loops and if statements, but a GUI program work completely differently. The main difference is that GUI programs are event driven.
With that being said, you want to choose a GUI framework, like Swing. Then decide if you want your application to be web based or desktop. An applet is more for web. If you want a desktop program, then you want a JFrame which will be the top-level container of your application.
You can learn all the components that are available to you in the standard Swing API here. IMO it seems like you need to start from the beginnging, so I would start from the very being of How to Create GUIs with Swing. You will want to pay close attention to section on Writing Event Listeners
If you do want to create an Applet instead of a desktop program, you can see the Applets, where you'll learn how to develop Applets and how to deploy them. You will still need to learn some basics though from the Swing link I mentioned.
Also, before you start using drag and drop gui builder tools, I would strongly urge you to first learn to hand code. It will work best for you in the long run.
I hope this gets you started in the right direction.

The defacto world standard GUI for all platforms is becoming Html5 and css3.
So the easiest way for you to write an interface is in HTML. You don't need an applet unless you have real specific needs like having a constant connection to the server for a chat or whatever. Anyway most of the applet reasons to exist are now resolved in standard HTML. If you want to learn a new langue, try Dart (dartlang.org)
You could use dart to have the more adaptable GUI to standards in the world
I explain why in this blog post
http://1veu.blogspot.com/2013/12/why-i-think-dart-will-detrone-java.html
Naturally even if you need to write a stand alone application with native GUI, HTML5 and css3 are still widely employed along with webkit or native code transformers like PhoneGap.

Adding components to the palette in NetBeans GUI Builder

I have created some custom JPanel classes using the NetBeans GUI Builder. Next, I added them to the palette. Then I created a custom JFrame and was able to drag my JPanels onto the JFrame. This worked great while I was simply working on the GUI front end. Now I am working on the backend logic, which includes some JDBC code. I have created a BaseballCardIO interface and implemented it in BaseballCardJDBCIO to centralize all the the database stuff.
Now, one of my JPanels, AddCardsPanel, needs a reference to one of these BaseballCardIOs. I started by creating one directly in the AddCardsPanel constructor. (I know, not the best design decision anyway...) Everything was working great until I open my JFrame class in NetBeans. It started to complain about not finding the JDBC driver class.
I want to continue to use the NetBeans GUI Builder for now. I have two solutions in mind to fix my problem:
1) Tell NetBeans where to find the JDBC driver and keep the code as-is. How do I do this?
2) Modify my design so that AddCardsPanel has a constructor which takes a BaseballCardIO as a parameter. This would actually be preferrable since it makes more sense for someone else to be responsible for creating the BaseballCardIO, not AddCardsPanel. However, I still need AddCardsPanel to play nicely with NetBeans GUI Builder, which means that it needs a no-args constructor. I imagine that I could add some code which detects if AddCardsPanel is being used as a JavaBean by NetBeans then the JFrame calls the noargs constructor. Otherwise, if my application is actually running, then the JFrame calls other constructor and sends it a BaseballCardIO.
Is this a good way to go? Or does anyone have any other possible solutions?

Add the driver JAR to NetBeans as a library, shown here, and to your project, shown here.
In Window > Services > Database > New Connections, fill out the required fields.
Don't let the NetBeans GUI builder dictate your design. Isolate database access to your TableModel and other component models.
Edit your question to include an sscce that shows any problems you encounter; a .form should not be required.

Genome browser built in java: Swing and awt or Swing and Processing?

I'm writing a genome browser designed primarily to view the history of chromosomal rearrangements. Right now the project is a series of proof-of-concept demos written using Processing. At this point if I don't make any radical changes the final application will be a web applet with a gui built of swing components that open PApplets to actually show the rearrangements happening.
My question is: Should I give up on processing and switch over to pure Swing/AWT? This is my first big java project. I'm building in eclipse, but I can use netbeans as well. If I could embed PApplet objects inside a JFrame, for example, that would make my day.

processing.core.PApplet extends java.applet.Applet, so it should be possible to embed
a PApplet in a java.awt.Frame, as discussed in the article Applet ⇒ application: Hybrid Switch Hitters. See also, Mixing heavy and light components.
Addendum: From the API, "Processing runs in a Frame and not a JFrame. However, there's nothing to prevent you from embedding a PApplet into a JFrame," except for the limitations mentioned above.

Keep in mind that I know almost nothing about either Processing or your project, so I can only give you general advice.
The question that you should ask yourself before every major design change: what problem am I trying to solve by making this change? If the current architecture works, then you should keep it. If it's not working, then you should start by defining the specific things that are wrong with it (which I notice you didn't do).

Java: Adding a User Interface to a program

If I have Java program and I need to alter it to an interface and include icons,
is there any easy I can do this and is there a good application that can help me to do it ?
or do I have to code it in myself?

Nop, /me thinks ur need 1337 mad Java programin' skillz!
Translation for the rest of the world: Sorry, you'll need to program in Java.
Added: Hey, what's with the downvotes? He started it! :P Besides - no matter if he wants to add or modify (the original text wasn't clear on this) the UI of a Java program, he will need to program in Java to bring his UI together with the code. There is no miracle tool that can allow you to draw an UI and it will suddenly do what you do.

Netbeans has a Swing GUI Builder. Quoting from their website. Let's hope this doesn't count has hidden advertising :)
Design Swing GUIs by dragging and
positioning GUI components from a
palette onto a canvas. The GUI builder
automatically takes care of the
correct spacing and alignment. Click
into JLabels, JButtons, ButtonGroups,
JTrees, JTextFields, ComboBoxes and
edit their properties directly in
place. You can use the GUI builder to
prototype GUIs right in front of
customers.

If you want to add a UI to your Java program there are tools to help you, such as the Swing GUI Builder inside of IntelliJ Idea. However, you're still going to have to write the appropriate code to hook into the UI.

It's just a website? Well depending on whether it uses CSS you might be able to just modify a .css file. This will only let you modify how the site looks as opposed to works.
See here for an example of how this technology works. However this depends on how css-dependent the website is and it's possible you may still run into some difficulties.

You want to use a Java framework to help you with the UI. For example, you can use JSF (Javaserver faces), which allows you to drag and drop components for a UI onto the site. Otherwise, you can use web programs such as Dreamweaver to design the UI, before coding the backend logic yourself in java.