How to use

getExpWithInteractionsContainingAnnotation

method

in

uk.ac.ebi.intact.application.dataConversion.dao.ExperimentListGeneratorDao

/**
 * 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." );
}