private Set<EvidenceCodeVocabulary> getEvidenceCodes(ExperimentDescription experimentDescription) { Set<EvidenceCodeVocabulary> toReturn = new HashSet<EvidenceCodeVocabulary>(); // get experiment methods Set<CvType> cvTypeSet = new HashSet<CvType>(3); //skip if "unspecified method" (MI:0686) is the interaction detection method if(experimentDescription.getInteractionDetectionMethod() != null && !"MI:0686".equalsIgnoreCase(experimentDescription.getInteractionDetectionMethod().getXref().getPrimaryRef().getId())) cvTypeSet.add(experimentDescription.getInteractionDetectionMethod()); if(experimentDescription.getParticipantIdentificationMethod() != null && !"MI:0686".equalsIgnoreCase(experimentDescription.getParticipantIdentificationMethod().getXref().getPrimaryRef().getId())) cvTypeSet.add(experimentDescription.getParticipantIdentificationMethod()); if(experimentDescription.getFeatureDetectionMethod() != null && !"MI:0686".equalsIgnoreCase(experimentDescription.getFeatureDetectionMethod().getXref().getPrimaryRef().getId())) cvTypeSet.add(experimentDescription.getFeatureDetectionMethod()); // create openControlledVocabulary objects for each detection method for (CvType cvtype : cvTypeSet) { EvidenceCodeVocabulary ecv = findOrCreateControlledVocabulary(cvtype, EvidenceCodeVocabulary.class); if (ecv != null) toReturn.add(ecv); } return toReturn; }
CrossReference detection = cvConverter.toMitab(experiment.getInteractionDetectionMethod());
if ( mExperimentDescription.getInteractionDetectionMethod() != null ) { jExperimentDescription.setInteractionDetectionMethod( cvTypeConverter.toJaxb( mExperimentDescription.getInteractionDetectionMethod() ) );
if ( mExperimentDescription.getInteractionDetectionMethod() != null ) { jExperimentDescription.setInteractionDetectionMethod( cvTypeConverter.toJaxb( mExperimentDescription.getInteractionDetectionMethod() ) );
InteractionDetectionMethod idm = psiObject.getInteractionDetectionMethod(); if (idm != null){ CvInteraction cvInteractionDetectionMethod = this.interactionDetectionMethodConverter.psiToIntact(idm);