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Hello Brandon,
 Good to hear from you. Tony had written an
example some time ago to do just this. I'm 
including a slightly modified version of the
class which can read in an sio file, process
the events with an example processor and write
out the histograms into an aida file which can be 
further analyzed with JAS3. It's not as clean as
we'd like it to be, but it should allow you to 
proceed with your analysis.
 I'm appending the requisite setup to configure
your system to compile and run. You'll have to 
modify the locations of your installation. Please
let me know if you encounter any difficulties
or have any further questions.
 By the way, we have set up a discussion forum
to supplant this mailing list. Please visit
http://forum.linearcollider.org and provide us
with some feedback.

Norman



set JAS3LCD=c:\documents and settings\tonyj\.jas3\extensions
set JAS3ROOT=c:\Program Files\jas3\lib
set JAS3EXT=c:\Program Files\jas3\extensions

set CLASSPATH=.
set CLASSPATH=%CLASSPATH%;%JAS3ROOT%\freehep-base.jar
set CLASSPATH=%CLASSPATH%;%JAS3ROOT%\jas3.jar
set CLASSPATH=%CLASSPATH%;%JAS3ROOT%\openide-lookup.jar
set CLASSPATH=%CLASSPATH%;%JAS3ROOT%\jdom.jar
set CLASSPATH=%CLASSPATH%;%JAS3ROOT%\jas-plotter.jar
set CLASSPATH=%CLASSPATH%;%JAS3EXT%\aida.jar
set CLASSPATH=%CLASSPATH%;%JAS3EXT%\aida-dev.jar
set CLASSPATH=%CLASSPATH%;%JAS3EXT%\freehep-hep.jar
set CLASSPATH=%CLASSPATH%;%JAS3LCD%\jas3lcd.jar
set CLASSPATH=%CLASSPATH%;%JAS3LCD%\lcd.jar

javac StandaloneJas3SioAnalyzer.java
java StandaloneJas3SioAnalyzer MyFile.sio -1