Interfacing Java with the command prompt

Hi everyone,
I'm very new to java and wanted to see if anyone had any advice before i started getting too far into this project. I want to write a java program which allows the user to draw lines on the screen, and move them around, and then the program will compute the equations of these lines and feed them into another program to study the algebra behind the geometry.
I've written an applet which is a start towards what I want: http://math.berkeley.edu/~aboocher/Mouse2.html but I'm encountering problems since it seems very difficult to have an applet write to a file, so I started trying to just create a self-contained java program. Before I move further I was hoping someone could point me in the right direction.
Ultimately I would like a window where the user can draw some geometric objects and the computer will write the equations to a file and then when I click "compute" say, it will run my other program (which can be done from the command line) and display "true or false"
In case it matters, I'm on a Mac and the exterior program is called Macaulay 2.
Thanks for your help!

That seems highly reasonable.
If your going to be writing to a file, it would probably be a better approach to create an application.
As for the arithmetic part of it, you'll want to save the points that the lines dropped, to use for future calculations. Using arrays would probably be a good idea.
You'll also want to reduce the flickering problem with your applet on the website you linked to. Maybe double buffer? Along with using arrays to recall previous lines

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