The other posts describe what a stack trace is, but it can still be hard to work with.
If you get a stack trace and want to trace the cause of the exception, a good start point in understanding it is to use the Java Stack Trace Console in Eclipse. If you use another IDE there may be a similar feature, but this answer is about Eclipse.
First, ensure that you have all of your Java sources accessible in an Eclipse project.
Then in the Java perspective, click on the Console tab (usually at the bottom). If the Console view is not visible, go to the menu option Window -> Show View and select Console.
Then in the console window, click on the following button (on the right)
and then select Java Stack Trace Console from the drop-down list.
Paste your stack trace into the console. It will then provide a list of links into your source code and any other source code available.
This is what you might see (image from the Eclipse documentation):
The most recent method call made will be the top of the stack, which is the top line (excluding the message text). Going down the stack goes back in time. The second line is the method that calls the first line, etc.
If you are using open-source software, you might need to download and attach to your project the sources if you want to examine. Download the source jars, in your project, open the Referenced Libraries folder to find your jar for your open-source module (the one with the class files) then right click, select Properties and attach the source jar.