private static <C extends CvType> C createCvType(Class<C> cvTypeClass, String name) { C cv; try { cv = cvTypeClass.newInstance(); cv.setNames(createNames(name, null)); } catch (Exception e) { throw new IllegalArgumentException("Is this a cvType?: "+cvTypeClass, e); } return cv; }
public static Interaction createInteraction(String name, ExperimentDescription experiment, InteractionType interactionType, Collection<Participant> participants) { Interaction interaction = new Interaction(); assignNextId(interaction); interaction.setNames(createNames(name, null)); for (Participant participant : participants) { interaction.getParticipants().add(participant); } interaction.getInteractionTypes().add(interactionType); interaction.getExperiments().add(experiment); return interaction; }
public static Organism createOrganism(int taxid, String name) { Organism organism = new Organism(); organism.setNames(createNames(name, null)); organism.setNcbiTaxId(taxid); return organism; }
public static Feature createFeature(String name, FeatureType featureType, Collection<Range> ranges) { Feature feature = new Feature(); assignNextId(feature); feature.setNames(createNames(name, name)); feature.getRanges().addAll(ranges); feature.setFeatureType(featureType); return feature; }
public static ExperimentDescription createExperiment(String name, String publicationId, InteractionDetectionMethod interactionDetectionMethod, ParticipantIdentificationMethod participantIdentificationMethod, Organism hostOrganism) { ExperimentDescription experiment = new ExperimentDescription(); assignNextId(experiment); experiment.setNames(createNames(name, null)); experiment.setBibref(createBibrefPubmed(publicationId)); experiment.setInteractionDetectionMethod(interactionDetectionMethod); experiment.setParticipantIdentificationMethod(participantIdentificationMethod); experiment.getHostOrganisms().add(hostOrganism); return experiment; }
public static Source createSource(String name, String description, String sourcePublicationId, String miId) { Source source = new Source(); Names names = createNames(name, description); source.setNames(names); if (miId != null) { Xref miRef = createXrefPsiMi(miId); source.setXref(miRef); } if (sourcePublicationId != null) { source.setBibref(createBibrefPubmed(sourcePublicationId)); } return source; }
public static Interactor createInteractor(String primaryId, String dbMi, InteractorType interactorType, Organism organism) { Interactor interactor = new Interactor(); assignNextId(interactor); interactor.setNames(createNames(primaryId, null)); interactor.setInteractorType(interactorType); interactor.setOrganism(organism); interactor.setXref(createXrefIdentity(primaryId, dbMi, dbMi)); return interactor; }