Preliminary

Often times your analysis is going to involve more than one input file. Rather than running over each input file by loading it manually into JAS3 and saving the output files, concatenating the resulting files by hand, here is an easy way to save the result of an analysis that runs over a number of files in one go.

Using a script to combine all your input files

The following jython snippet can be loaded into JAS3. Simply execute it with <F2>.
This assumes that your analysis is carried out by the module TrackTester which you should have loaded into JAS3 and compiled already. (If TrackTester is a jython Module, the compilation step is of course omitted.) You can of course add any number of additional modules to the loop.
After the loop has finished, the output of the analysis is saved in AIDA format. This assumes that you are putting the results of your analysis into the AIDA.defaultinstance() in org.lcsim.

#! /usr/bin/env jython
import sys
from java.io import File
#from org.lcsim.util import Driver
from org.lcsim.util.aida import AIDA
from org.lcsim.util.loop import LCIODriver
from org.lcsim.util.loop import LCSimLoop
from org.lcsim.mc.fast import MCFast
from java.lang import System
import TrackTester

loop = LCSimLoop()
loop.add(MCFast())
loop.add(TrackTester())
for number in range(2):
    input = File('TrackingStudies/pythiaWWnunubar-%d-500.stdhep' % number)
    loop.setStdhepRecordSource(input, 'sid01')
    loop.loop(-1)
AIDA.defaultInstance().saveAs('TrackingStudies/pythiaWWnunubar.aida')
loop.dispose()