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src/m/g/mgtaxa-HEAD/MGT/DirStore.py   mgtaxa(Download)
        opt.mode = "trainScatter"
        app = ClassifierApp(opt=opt)
        opt = app.getOpt() #get the missing options filled with defaults
        # we need to clean up the models directory otherwise we run a danger
        # of picking up old models that are not trained in this session
        rmrf(self.getFilePath(opt.modelRoot))
        jobs = app.run(**kw)
        opt.mode = "test"
        app = ClassifierApp(opt=opt)
        opt = app.getOpt() #get the missing options filled with defaults
        opt.mode = "trainScatter"
        app = ClassifierApp(opt=opt)
        opt = app.getOpt() #get the missing options filled with defaults
        # we need to clean up the models directory otherwise we run a danger
        # of picking up old models that are not trained in this session
        opt.mode = "predict"
        app = ClassifierApp(opt=opt)
        opt = app.getOpt() #get the missing options filled with defaults
        jobs = app.run(**kw)
        self.save()

src/m/g/mgtaxa-HEAD/MGT/CrossValidatorApp.py   mgtaxa(Download)
        spOptFile = self.getSplitOptFileName(testSplit)
        spApp = ClassifierApp(opt=spClOpt)
        spClOpt = spApp.getOpt() #get the missing options filled with defaults
        #that just saves a copy for us - App will create its own when it 
        #submits a batch job (unique and slightly modified)