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For example, Eclipse.  You make a breakpoint at line 3, and click the bug.  It shows an alternate window in which there is another button called Step Over. Click it and it will execute just line three. Click again and it will execute line 4.  Keep clickign and you'll work down as far as you want...plus it shows what was executed at each line.

In my Java class we're supposed to step through the code by hand and write the output of the text in order that it is executed.

 

A good discipline. That's exactly what should be going on your head when you are writing the code.

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