public Interaction createInteraction(Interactor ... interactors) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); Experiment experiment = createExperimentEmpty(); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experiment)), cvInteractionType, intType, "temp", getInstitution()); Component[] components = new Component[interactors.length]; for (int i=0; i<interactors.length; i++) { components[i] = createComponentNeutral(interaction, interactors[i]); components[i].setInteraction(null); } return createInteraction(components); }
public Interaction createInteraction(Interactor ... interactors) { CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION); Experiment experiment = createExperimentEmpty(); CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION ); Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experiment)), cvInteractionType, intType, "temp", getInstitution()); Component[] components = new Component[interactors.length]; for (int i=0; i<interactors.length; i++) { components[i] = createComponentNeutral(interaction, interactors[i]); components[i].setInteraction(null); } return createInteraction(components); }
/** * This creates a stable (non-random) interaction */ public Interaction createDeterministicInteraction() { Interaction interaction = createInteraction("fooprey-barbait", createDeterministicProtein("A2", "barbait"), createDeterministicProtein("A1", "fooprey"), createDeterministicExperiment()); interaction.getAnnotations().add(createAnnotation("This is an annotation", CvTopic.COMMENT_MI_REF, CvTopic.COMMENT)); CvFeatureType featureType = createCvObject(CvFeatureType.class, CvFeatureType.EXPERIMENTAL_FEATURE_MI_REF, CvFeatureType.EXPERIMENTAL_FEATURE); Feature feature = createFeature("feature1", featureType); feature.setComponent(null); Range range = createRange(1, 1, 5, 5); feature.addRange(range); interaction.getComponents().iterator().next().addBindingDomain(feature); // interaction.getComponents().iterator().next().addComponentParameter(createDeterministicComponentParameter()); // interaction.addXref(createPrimaryReferenceXref( interaction , "testreference")); interaction.addConfidence( createDeterministicConfidence()); interaction.addParameter( createDeterministicInteractionParameter() ); return interaction; }
/** * This creates a stable (non-random) interaction */ public Interaction createDeterministicInteraction() { Interaction interaction = createInteraction("fooprey-barbait", createDeterministicProtein("A2", "barbait"), createDeterministicProtein("A1", "fooprey"), createDeterministicExperiment()); interaction.getAnnotations().add(createAnnotation("This is an annotation", CvTopic.COMMENT_MI_REF, CvTopic.COMMENT)); CvFeatureType featureType = createCvObject(CvFeatureType.class, CvFeatureType.EXPERIMENTAL_FEATURE_MI_REF, CvFeatureType.EXPERIMENTAL_FEATURE); Feature feature = createFeature("feature1", featureType); feature.setComponent(null); Range range = createRange(1, 1, 5, 5); feature.addRange(range); interaction.getComponents().iterator().next().addBindingDomain(feature); // interaction.getComponents().iterator().next().addComponentParameter(createDeterministicComponentParameter()); // interaction.addXref(createPrimaryReferenceXref( interaction , "testreference")); interaction.addConfidence( createDeterministicConfidence()); interaction.addParameter( createDeterministicInteractionParameter() ); return interaction; }