/** * * @param interaction : the interaction to expand * @return the complex generated from this interaction instance */ protected Complex createComplexEntity(T interaction) { String complexName = generateComplexName(interaction); Complex interactionAsComplex = getInteractorFactory().createComplex(complexName, null); InteractorCloner.copyAndOverrideBasicComplexPropertiesWithInteractionProperties(interaction, interactionAsComplex); return interactionAsComplex; }
interactor = getInteractorFactory().createInteractorFromInteractorType(type.iterator().next(), shortName); interactor = getInteractorFactory().createInteractorFromIdentityXrefs(uniqueId, shortName); interactor = getInteractorFactory().createInteractorFromIdentityXrefs(altid, shortName); interactor = getInteractorFactory().createInteractor(shortName, null); interactor = getInteractorFactory().createInteractor(shortName, null); interactor = getInteractorFactory().createInteractorFromIdentityXrefs(altid, shortName); interactor = getInteractorFactory().createInteractor(shortName, null); interactor = getInteractorFactory().createInteractor(shortName, null);
protected void processInteractorPool(Collection<MitabXref> xref, InteractorPool interactor) { InteractorPool pool = (InteractorPool)interactor; for (Xref ref : xref){ // we have a component of the interactor pool if (XrefUtils.doesXrefHaveQualifier(ref, Xref.INTERACTOR_SET_QUALIFIER_MI, Xref.INTERACTOR_SET_QUALIFIER)){ Interactor subInteractor = interactorFactory.createInteractorFromDatabase(ref.getDatabase(), ref.getId().toLowerCase()); if (subInteractor != null){ subInteractor.getIdentifiers().add(new MitabXref(ref.getDatabase(), ref.getId(), ref.getVersion(), CvTermUtils.createIdentityQualifier())); ((MitabInteractor)subInteractor).setSourceLocator(((MitabXref)ref).getSourceLocator()); } // create a default interactor else{ subInteractor = interactorFactory.createInteractor(ref.getId().toLowerCase(), CvTermUtils.createUnknownInteractorType()); subInteractor.getIdentifiers().add(new MitabXref(ref.getDatabase(), ref.getId(), ref.getVersion(), CvTermUtils.createIdentityQualifier())); ((MitabInteractor)subInteractor).setSourceLocator(((MitabXref)ref).getSourceLocator()); } // add the component to the interactor pool pool.add(subInteractor); } // we have a simple xref else{ pool.getXrefs().add(ref); } } }
interactor = getInteractorFactory().createInteractor(MitabUtils.UNKNOWN_NAME, null); ((FileSourceContext)interactor).setSourceLocator(new MitabSourceLocator(line, column, mitabColumn)); hasInteractorDetails = false;
interactor = getInteractorFactory().createInteractor(MitabUtils.UNKNOWN_NAME, null); ((FileSourceContext)interactor).setSourceLocator(new MitabSourceLocator(line, column, mitabColumn)); hasInteractorDetails = false;
interactor = getInteractorFactory().createInteractor(MitabUtils.UNKNOWN_NAME, null); ((FileSourceContext)interactor).setSourceLocator(new MitabSourceLocator(line, column, mitabColumn)); hasInteractorDetails = false;