inputAS = document.getAnnotations();
// load the pipeline and extractor
pipeline = (ConditionalSerialAnalyserController)
PersistenceManager.loadObjectFromUrl(path2xgapp);
extractor = new GroovyPreprocessor(path2rules);
sequences = new ArrayList<SequenceInstance>();
xAlphabet = new Alphabet();
yAlphabet = new Alphabet();
this.path2xgapp = path2xgapp;
}