@Override public void process(JCas cas) throws AnalysisEngineProcessException { String text = cas.getDocumentText(); List<Mention> mentions = matcher.match(text); for (Mention mention : mentions) { String mostProbableID = mention.getMostProbableID(); String idsToString = mention.getIdsToString(); LinnaeusSpecies species = new LinnaeusSpecies(cas); species.setBegin(mention.getStart()); species.setEnd(mention.getEnd()); species.setMostProbableSpeciesId(mostProbableID); species.setAllIdsString(idsToString); species.setAmbigous(mention.isAmbigous()); species.addToIndexes(); } }