To run the main method of a project, select "Project, Run Main Class." This will load the class specified as the project's main class in Project Properties, and run its main method. If you have not specified the file to load in Project Properties, this option is grayed out
If you have configured a main class, then DrJava will also show a "Run Project" toolbar button. If you have not specified a class as main class, a "Run" button is shown instead that runs the main method of the currently shown document.