@Override protected Component syncAttributes(Component intactObject) { if (intactObject.getExpressedIn() != null) { BioSource bioSource = BioSourcePersister.getInstance().syncIfTransient(intactObject.getExpressedIn()); intactObject.setExpressedIn(bioSource);
sb.append(createUniquenessString(component.getExpressedIn()));
sb.append(createUniquenessString(component.getExpressedIn()));
if ( component.getExpressedIn() != null ) { Element hostOrganismList = session.createElement( "hostOrganismList" ); element.appendChild( hostOrganismList );
if ( component.getExpressedIn() != null ) { Element hostOrganismList = session.createElement( "hostOrganismList" ); element.appendChild( hostOrganismList );
component.setExpressedIn( synchronize( component.getExpressedIn() ) ); component.setInteraction( synchronize( component.getInteraction() ) ); component.setInteractor( synchronize( component.getInteractor() ) );
if ( component.getExpressedIn() != null && component.getInteractor().getBioSource() != null) { Element hostOrganismList = session.createElement( "hostOrganismList" ); element.appendChild( hostOrganismList );
component.setExpressedIn( synchronize( component.getExpressedIn() ) ); component.setInteraction( synchronize( component.getInteraction() ) ); component.setInteractor( synchronize( component.getInteractor() ) );
@Override protected void saveOrUpdateAttributes(Component intactObject) throws PersisterException { super.saveOrUpdateAttributes(intactObject); if (intactObject.getExpressedIn() != null) { BioSourcePersister bioSourcePersister = BioSourcePersister.getInstance(); bioSourcePersister.saveOrUpdate(intactObject.getExpressedIn()); } CvObjectPersister cvPersister = CvObjectPersister.getInstance(); cvPersister.saveOrUpdate(intactObject.getCvBiologicalRole()); cvPersister.saveOrUpdate(intactObject.getCvExperimentalRole()); for (CvIdentification participantDetection : intactObject.getParticipantDetectionMethods()) { cvPersister.saveOrUpdate(participantDetection); } for (CvExperimentalPreparation experimentalPreparation : intactObject.getExperimentalPreparations()) { cvPersister.saveOrUpdate(experimentalPreparation); } InteractionPersister.getInstance().saveOrUpdate(intactObject.getInteraction()); InteractorPersister.getInstance().saveOrUpdate(intactObject.getInteractor()); for (Feature feature : intactObject.getBindingDomains()) { FeaturePersister.getInstance().saveOrUpdate(feature); } }
if (intactObject.getExpressedIn() != null) { Organism organism = organismConverter.intactToPsi(intactObject.getExpressedIn()); if (organism != null) { HostOrganism hostOrganism = new HostOrganism();
protected void traverseComponent(Component component, IntactVisitor ... visitors) { if (component == null) return; for (IntactVisitor visitor : visitors) { visitor.visitComponent(component); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(component)) { return; } traverse(component.getInteraction(), visitors); traverse(component.getInteractor(), visitors); traverse(component.getCvBiologicalRole(), visitors); traverse(component.getExpressedIn(), visitors); traverse(component.getParameters(), visitors); traverse(component.getParticipantDetectionMethods(), visitors); traverse(component.getExperimentalPreparations(), visitors); traverse(component.getBindingDomains(), visitors); traverse(component.getExperimentalRoles(), visitors); }
protected void traverseComponent(Component component, IntactVisitor ... visitors) { if (component == null) return; for (IntactVisitor visitor : visitors) { visitor.visitComponent(component); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(component)) { return; } traverse(component.getInteraction(), visitors); traverse(component.getInteractor(), visitors); traverse(component.getCvBiologicalRole(), visitors); traverse(component.getExpressedIn(), visitors); traverse(component.getParameters(), visitors); traverse(component.getParticipantDetectionMethods(), visitors); traverse(component.getExperimentalPreparations(), visitors); traverse(component.getBindingDomains(), visitors); traverse(component.getExperimentalRoles(), visitors); }
clone.setExpressedIn(clone(component.getExpressedIn()));
if (!expressedIn.equals( component.getExpressedIn() )){ return false; else if (component.getExpressedIn() != null){ return false;
if (!expressedIn.equals( component.getExpressedIn() )){ return false; else if (component.getExpressedIn() != null){ return false;
clone.setExpressedIn(clone(component.getExpressedIn()));