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How to edit library source files on NetBeans?

I am doing JAVA project based on the SSJ (Stochastic Simulation in Java) libraries. In my project I have followed the required steps to import the SSJ library files and also the source files.
When looking at the SSJ library files in the project's Libraries branch, only class files appear shown, but when I open them I can view the source code (which I couldn't before, as I hadn't imported the sources) so I assume everything was imported correctly.
When I run the examples provided with the library everything runs fine and as expected. But if I try to change the source code for the libraries for instance, changing the text on an output, the changes I make to the source files aren't reflected in the output from the java programs.
Any hint on what I might be doing wrong?
I understand this might be hard to understand or test as I can't quite create and SSCCE for this matter. The library files are hosted here (http://www.iro.umontreal.ca/~simardr/ssj/ssj-20120216.zip) and the source code here (http://www.iro.umontreal.ca/~simardr/ssj/ssj-source.html).
Thanks in advance for all your help!

Adding source to libraries it's for debugging and documentation purposes. It does not mean that Netbeans will detect changes and recompile classes automatically.
You should create a project for the library itself to recreate it from source. Changes are that if you have the source there will be a build.xmlor a pom.xml that contains the steps to compile the library and will allow to create a Java Free Form Project or a Project with existing POM.
You'd then remove the reference to library itself and add a dependency to the project.
Other option would be to add the library source to the same project you are using (and, again, removing reference to the library) but I would not recommend this unless it's a very small simple library.
EDIT. Particular ssj information.
ssj is a library where the original source code is in .tex files and it requires several programs available to generate .java files and then compile them. All this information can be found in the COMPILE.txt original file.
Since the source distribution includes .java files it is possible to generate a .jar just using Netbeans but it requires to modify the build.xml to just compile Java source files. Also when creating the Java Free Form Project is necessary to select lib as the target to Build Project.
Here it's a minimal build xml for Netbeans 7.1 to compile from Java sources.

In order to create the new *.java file from the *.tex file, you need the tcode.jar which is available in the distribution. Have you added tcode.jar as an external jar to your project?
umontreal.iro.lecuyer.tcode.Texjava is in tcode.jar

restore project from jar file

first i'd like to point out that im fairly new to netbeans and java, couldnt exactly find what i need on the web.
I downloaded a software's source files and was modifying it on netbeans. naturally when building the project, netbeans creates in (for example) documents/project_folder/dist/ a lib folder and the finished JAR file that i can use.
if i delete by mistake the source files, and would like to apply all the changes i previously made to fresh source files using the JAR and lib folder i still have, is it possible and how?

First of all it is not possible to get a source again from jar file in lib folder. Jar file is executable file which will just contain class files. You can use java decompilers to get source again.

NB do not has a version control nor auto save by default. You may have a look on git in NB7.
When you restore from Jar with decompiler there is a big chance to get the source back, even more if you know what your code is all about.

You can get the source back by using some decompiler. There are many decompilers available like DJ Decomipler. My favourite is Jd Java Decompiler. Its very small in size and does its job pretty well

I'm rather an Eclipse user but I guess both Eclipse and Netbeans are similar to a certain extent. Unless the jar has been created including the source, you won't have other choices that decompile the class files.
When needed, I usually go with JD-GUI which does a pretty good job decompiling jars.

It is not possible to retrieve exact source code from a compiled byte code. But there is a possibility to recover your code to some extent
JD is a good Java decompiler.
http://java.decompiler.free.fr/?q=jdgui
I think JD is a super hero in cases that the original source code is lost.

Keep your source code on any SCM. Use remote SCM not to loose your code. See: google code, github, launchpad etc.

Trouble installing Boilerpipe

This is the third time I've installed it. I had it working on Windows, and up until a few days ago on Linux. I've done all I can do and I don't understand how to run this Java program.
The source code is a folder with a lib, src some jars and a classpath and project file.
The classpath file makes some declarations like classpathentry=src/main and path=lib, path=src.
All of these make sense. There is a folder 'main' inside 'src'.
The tiny file I'm trying to run starts off by
import de.l3s.boilerpipe.demo
I'm trying to run 'Oneliner.java'. I cannot compile it.
No matter what/where that class file is, I cannot run it. It results in a noclassdeffound.
I've run it in the main, the src, the root, the demo, the ... anywhere.
I've tried compiling it in different directories, running it with various java command line switches that were recommended. Supposedly you can have it 'search' for the file, which I've yet to experience. The sheer stubbornness of this java environment is terrifying. And massively humiliating for me.

I had the same problem with installing it. The 'Getting Started' page is poor quality.
My solution was to use a python wrapper, which you can find here: https://github.com/misja/python-boilerpipe
It takes care of all of the dependencies you'll need (however, you might be missing jpype if you're on a Mac. In that case, you'll need to install it manually from: http://jpype.sourceforge.net/).

The best way to start using the boilerpipe algorithm (and to see what it is for) is to use the demo site:
http://boilerpipe-web.appspot.com/
If you want to integrate the boilerpipe library into your applications, or even intent to modify/improve the code, you will definitely need solid Java programming skills.
As a quick-start I suggest that you install a recent version of the Eclipse IDE for Java Developers and import boilerpipe-core as a project. This avoids pretty much of the classpath configuration, and almost everything should be set up correctly for you.
The classpath file you mentioned is probably ".classpath", which is part of the Eclipse project configuration. You don't need it unless you want an Eclipse project.

Java JNA does not seem to be working

I recently downloaded the Java JNA from https://github.com/twall/jna/servlets/ProjectDocumentList?folderID=7408&expandFolder=7408&folderID=0 and tried using it. However, as exemplified by the screenshot below, the demo source code provided in https://github.com/twall/jna/ won't compile, no matter where I place the files. Mind you, I've tried placing them both in the default package an every other combination of package mix-ups, and this is only the latest version. Does anybody know why the compiler can't find what is contained within the JAR file? (Also, as you can see, the class files are all in the jar file to be found)

Basically, the JAR should go in the classpath. In Netbeans, you can do it by adding it as library to the build path of the project through the project properties.

How do you use a Java Library?

I'm trying to use an open source java library to visualize nodes and edges in a graph, but I'm completely lost.
I have a bunch of jar files in a folder. Clicking on some of the jar files makes java swing windows pop open with graphs displayed. Clicking other jar files does nothing.
If I figured that out, would I just stick the jar files in there with the other ones, or would that still not work?
And if I ever figure out how to use these files, does that mean that I have to include them if I transfer my java project to another computer? How would I go about doing that?

I believe if you put the jars in your classpath, you can import and use classes just like you would a standard library. Figuring out the classpath can be confusing, but you can just set it when you start your jvm. Your IDE may have options for it, too.
Most java problems are classpath problems.

Have you included those libraries in your classpath?
If you are using eclipse, you could
Project - > properties -> Java build path ->addJar.
And the Jar file should be placed in a directory inside your workspace (lib/ for example)
If you have to take your project to another computer, you could take these steps
Before doing anything, export your project (as a Jar file, for example).
Save it into your favorite drive (cd / usb drive/ diskette/ tape).
On "the other" computer, you can import this project into your workspace

In Eclipse, you need to add libraries to the project build path.
In general, you need to provide dependencies via the classpath mechanisms at compile time and runtime. The precise mechanisms vary, but, for example, if you used the javac compiler, you would provide your libraries on the command line:
javac -classpath C:\dir\lib1.jar;C:\dir\lib2.jar foo/MyClass.java
These dependencies would also be required to invoke the app:
java -classpath C:\dir\lib1.jar;C:\dir\lib2.jar;. foo.MyClass
This page gives some good info, though googling for the term "classpath" should provide alternative sources.

You use it by including it in the classpath of your java application, that way you can reference it from your code. Here is a starter document. The JDK 1.6 has some easier options (such as specifying multiple jar files as *.jar). It is definitely a little complicated, but it is very worth knowing.

You should have documentation for these Jars. Some sounds like examples, but one must be the core graph modelling and rendering Jar. Hopefully the examples have source included.
Just add that Jar to your project in Eclipse (e.g., in a /lib folder in your project, then add it to the build path) and use the documentation to use the code. You can also use Eclipse to look inside the Jar file.
Unless there is no alternative, it probably isn't worth using a load of third party code that isn't documented at least on the API level, and without any source examples definitely not.