public static CvTerm getUnknownInteractorType() { if (unknownInteractorType == null){ unknownInteractorType = createUnknownInteractorType(); } return unknownInteractorType; }
public DefaultInteractor(String name, Organism organism){ this(name); this.organism = organism; this.interactorType = CvTermUtils.createUnknownInteractorType(); }
public void setInteractorType(CvTerm interactorType) { if (interactorType == null){ this.interactorType = CvTermUtils.createUnknownInteractorType(); } else { this.interactorType = interactorType; } }
public DefaultInteractor(String name, CvTerm type){ if (name == null || (name != null && name.length() == 0)){ throw new IllegalArgumentException("The short name cannot be null or empty."); } this.shortName = name; if (type == null){ this.interactorType = CvTermUtils.createUnknownInteractorType(); } else { this.interactorType = type; } }
public DefaultInteractor(String name){ if (name == null || (name != null && name.length() == 0)){ throw new IllegalArgumentException("The short name cannot be null or empty."); } this.shortName = name; this.interactorType = CvTermUtils.createUnknownInteractorType(); }
public DefaultInteractor(String name, String fullName, Xref uniqueId){ this(name, fullName); getIdentifiers().add(uniqueId); this.interactorType = CvTermUtils.createUnknownInteractorType(); }
public DefaultInteractor(String name, Xref uniqueId){ this(name); getIdentifiers().add(uniqueId); this.interactorType = CvTermUtils.createUnknownInteractorType(); }
public DefaultInteractor(String name, Organism organism, Xref uniqueId){ this(name, organism); getIdentifiers().add(uniqueId); this.interactorType = CvTermUtils.createUnknownInteractorType(); }
public DefaultInteractor(String name, String fullName, Organism organism, Xref uniqueId){ this(name, fullName, organism); getIdentifiers().add(uniqueId); this.interactorType = CvTermUtils.createUnknownInteractorType(); }
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); } } }