public Interaction createInteraction(String ... interactorShortLabels) { Interaction interaction = createInteractionDirect(); Protein prot = null; for (String interactorShortLabel : interactorShortLabels) { prot = createDeterministicProtein(interactorShortLabel, interactorShortLabel); createComponentNeutral(interaction, prot); } if (interactorShortLabels.length == 1) { createComponentNeutral(interaction, prot); } String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); return interaction; }
public Interaction createInteraction(String ... interactorShortLabels) { Interaction interaction = createInteractionDirect(); Protein prot = null; for (String interactorShortLabel : interactorShortLabels) { prot = createDeterministicProtein(interactorShortLabel, interactorShortLabel); createComponentNeutral(interaction, prot); } if (interactorShortLabels.length == 1) { createComponentNeutral(interaction, prot); } String shortLabel = InteractionUtils.calculateShortLabel(interaction); interaction.setShortLabel(shortLabel); 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; }
/** * 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; }