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 Participant createParticipant(Interactor interactor, BiologicalRole biologicalRole, ExperimentalRole experimentalRole) { Participant participant = new Participant(); assignNextId(participant); participant.setInteractor(interactor); participant.setBiologicalRole(biologicalRole); participant.getExperimentalRoles().add(experimentalRole); return participant; }
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 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; }