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Automating Windows from cygwin


I have some scientific instruments that will only talk to 
a proprietary Windows app, and some Linux programs that 
analyze the data. 
I would really like to automate the process of running the Windows
program so that the Linux programs could talk to cygwin over the net
and get the data.  
The problem is that the windows app was written long ago,
and source is not available.  So I am wondering if there
is a way to run an arbitrary windows application and do something
like mouse macros from cygwin.

Does anybody know of a way to do mouse macros from cygwin, or a way
to invoke menu items from a arbitrary windows app from cygwin, or a better way 
to approach this?  I have the impression that some people do mouse macros
via vnc.  Is there some O'Reilly book that I should have read?

Thanks!

- - --James Ganong



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