@Override public void process(JCas jCas) throws AnalysisEngineProcessException { int pmId = getHeaderIntDocId(jCas); DocumentSpecies docSpecies = selectSingle(jCas, DocumentSpecies.class); String msg = pmId + "\t" + docSpecies.getFamilyName(); for (LinnaeusSpecies species : select(jCas, LinnaeusSpecies.class)) { msg += "\t" + species.getMostProbableSpeciesId() + "\t" + species.getCoveredText().replaceAll("\t", " "); } LOG.debug(msg); }