public static Bibref createBibrefPubmed(String publicationId) { return createBibref(publicationId, "MI:0446", "pubmed"); }
public static BiologicalRole createBiologicalRoleUnspecified() { return createBiologicalRole("MI:0499", "unspecified role"); }
public static Participant createParticipantBait(Interactor interactor) { BiologicalRole biologicalRole = createBiologicalRoleUnspecified(); ExperimentalRole experimentalRole = createExperimentalRoleBait(); return createParticipant(interactor, biologicalRole, experimentalRole); }
public static Participant createParticipantPrey(Interactor interactor) { BiologicalRole biologicalRole = createBiologicalRoleUnspecified(); ExperimentalRole experimentalRole = createExperimentalRolePrey(); return createParticipant(interactor, biologicalRole, experimentalRole); }
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 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; }
public static ExperimentalRole createExperimentalRole(String mi, String name) { return createCvType(ExperimentalRole.class, mi, name); }
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 InteractorType createInteractorType(String mi, String name) { InteractorType intType = createCvType(InteractorType.class, name); intType.setXref(createXrefPsiMi(mi)); return intType; }
public static DbReference createDbReferenceIdentity(String primaryId, String dbAc, String dbName) { return createDbReference(primaryId, dbAc, dbName, "MI:0356", "identity"); }
public static ExperimentalRole createExperimentalRoleBait() { return createExperimentalRole("MI:0496", "bait"); }
public static EntrySet createEntrySet(PsimiXmlVersion version, Entry ... entries) { return createEntrySet(version, Arrays.asList(entries)); }
public static DbReference createDbReferencePsiMi(String psiMiRef) { DbReference ref = createDbReferenceIdentity(psiMiRef, "MI:0488", "psi-mi"); ref.setId(psiMiRef); return ref; }
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 ParticipantIdentificationMethod createParticipantIdentificationMethod(String mi, String name) { return createCvType(ParticipantIdentificationMethod.class, mi, name); }
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 <C extends CvType> C createCvType(Class<C> cvTypeClass, String miRef, String label) { C cv = createCvType(cvTypeClass, label); cv.setXref(createXrefPsiMi(miRef)); return cv; }
public static Xref createXrefIdentity(String primaryId, String dbMi, String dbName) { Xref xref = new Xref(); xref.setPrimaryRef(createDbReference(primaryId, dbMi, dbName, "MI:0356", "identity")); return xref; }
public static ExperimentalRole createExperimentalRoleUnspecified() { return createExperimentalRole("MI:0499", "unspecified role"); }