/** * Checks for a negative interaction. NB This will have to be done using SQL otherwise we end up materializing all * interactions just to do the check. * <p/> * Also the new intact curation rules specify that an Experiment should ONLY contain negative Interactions if it is * annotated as 'negative'. Thus to decide if an Experiment is classified as 'negative', the Annotations of that * Experiment need to be checked for one with a 'negative' Controlled Vocab attached to it as a topic. </p> * <p/> * However at some point in the future there may be a possibility that only the Interactions will be marked as * 'negative' (not the Experiment), and so these should be checked also, with duplicate matches being ignored. </p> * This method has to be static because it is called by the static 'classifyExperiments'. */ private void classifyNegatives() { negativeExperiments = new HashSet<Experiment>(); negativeExperiments.addAll( ExperimentListGeneratorDao.getExpWithInteractionsContainingAnnotation( CvTopic.NEGATIVE, searchPattern ) ); negativeExperiments.addAll( ExperimentListGeneratorDao.getContainingAnnotation( Experiment.class, CvTopic.NEGATIVE, searchPattern ) ); output.println( negativeExperiments.size() + " negative experiment found." ); }
/** * Checks for a negative interaction. NB This will have to be done using SQL otherwise we end up materializing all * interactions just to do the check. * <p/> * Also the new intact curation rules specify that an Experiment should ONLY contain negative Interactions if it is * annotated as 'negative'. Thus to decide if an Experiment is classified as 'negative', the Annotations of that * Experiment need to be checked for one with a 'negative' Controlled Vocab attached to it as a topic. </p> * <p/> * However at some point in the future there may be a possibility that only the Interactions will be marked as * 'negative' (not the Experiment), and so these should be checked also, with duplicate matches being ignored. </p> * This method has to be static because it is called by the static 'classifyExperiments'. */ private void classifyNegatives() { negativeExperiments = new HashSet<Experiment>(); negativeExperiments.addAll( ExperimentListGeneratorDao.getExpWithInteractionsContainingAnnotation( CvTopic.NEGATIVE, searchPattern ) ); negativeExperiments.addAll( ExperimentListGeneratorDao.getContainingAnnotation( Experiment.class, CvTopic.NEGATIVE, searchPattern ) ); log.debug( negativeExperiments.size() + " negative experiment found." ); }
/** * Checks for a negative interaction. NB This will have to be done using SQL otherwise we end up materializing all * interactions just to do the check. * <p/> * Also the new intact curation rules specify that an Experiment should ONLY contain negative Interactions if it is * annotated as 'negative'. Thus to decide if an Experiment is classified as 'negative', the Annotations of that * Experiment need to be checked for one with a 'negative' Controlled Vocab attached to it as a topic. </p> * <p/> * However at some point in the future there may be a possibility that only the Interactions will be marked as * 'negative' (not the Experiment), and so these should be checked also, with duplicate matches being ignored. </p> * This method has to be static because it is called by the static 'classifyExperiments'. */ private void classifyNegatives() { negativeExperiments = new HashSet<Experiment>(); negativeExperiments.addAll( ExperimentListGeneratorDao.getExpWithInteractionsContainingAnnotation( CvTopic.NEGATIVE, searchPattern ) ); negativeExperiments.addAll( ExperimentListGeneratorDao.getContainingAnnotation( Experiment.class, CvTopic.NEGATIVE, searchPattern ) ); output.println( negativeExperiments.size() + " negative experiment found." ); }