When you want to debug the Java code, set a breakpoint just before the node. Then, in the flow debugger, when the flow pauses at the breakpoint, you can step into the code, and then step through it (step over) line by line. You can also examine and change the Java variables.
This uses a combination of two perspectives: the Flow Debug perspective and the Debug Perspective. The workbench switches automatically between the two perspectives as required when you select the various debugging actions (and you can also switch between them yourself).
For more information on how to achieve this, see the related tasks links below.