public Component createComponent(Interaction interaction, Interactor interactor, CvExperimentalRole expRole, CvBiologicalRole bioRole) { Component component = new Component(getInstitution(), interaction, interactor, expRole, bioRole); CvIdentification cvParticipantDetMethod = createCvObject(CvIdentification.class, CvIdentification.PREDETERMINED_MI_REF, CvIdentification.PREDETERMINED); component.getParticipantDetectionMethods().add(cvParticipantDetMethod); CvExperimentalPreparation cvExperimentalPreparation = createCvObject(CvExperimentalPreparation.class, CvExperimentalPreparation.PURIFIED_REF, CvExperimentalPreparation.PURIFIED); component.getExperimentalPreparations().add(cvExperimentalPreparation); return component; }
/** * Retrieves the experimental preparations from a participant, initializing them if necessary. * Do not set the initialized collection of experimental preparations because cannot be orphan * @param component the component * @return The returned experimental preparations are ensured to be initialized * @since 2.4.0 */ public static Collection<CvExperimentalPreparation> ensureInitializedExperimentalPreparations(Component component) { Collection<CvExperimentalPreparation> expPrep; if (IntactCore.isInitialized(component.getExperimentalPreparations())) { expPrep = component.getExperimentalPreparations(); } else { expPrep = IntactContext.getCurrentInstance().getDaoFactory().getComponentDao().getExperimentalPreparationsForComponentAc(component.getAc()); } return expPrep; }
/** * Retrieves the experimental preparations from a participant, initializing them if necessary. * Do not set the initialized collection of experimental preparations because cannot be orphan * @param component the component * @return The returned experimental preparations are ensured to be initialized * @since 2.4.0 */ public static Collection<CvExperimentalPreparation> ensureInitializedExperimentalPreparations(Component component) { Collection<CvExperimentalPreparation> expPrep; if (IntactCore.isInitialized(component.getExperimentalPreparations())) { expPrep = component.getExperimentalPreparations(); } else { expPrep = IntactContext.getCurrentInstance().getDaoFactory().getComponentDao().getExperimentalPreparationsForComponentAc(component.getAc()); } return expPrep; }
public Component createComponent(Interaction interaction, Interactor interactor, CvExperimentalRole expRole, CvBiologicalRole bioRole) { Component component = new Component(getInstitution(), interaction, interactor, expRole, bioRole); CvIdentification cvParticipantDetMethod = createCvObject(CvIdentification.class, CvIdentification.PREDETERMINED_MI_REF, CvIdentification.PREDETERMINED); component.getParticipantDetectionMethods().add(cvParticipantDetMethod); CvExperimentalPreparation cvExperimentalPreparation = createCvObject(CvExperimentalPreparation.class, CvExperimentalPreparation.PURIFIED_REF, CvExperimentalPreparation.PURIFIED); component.getExperimentalPreparations().add(cvExperimentalPreparation); ComponentParameter componentParameter = createDeterministicComponentParameter(); component.addParameter(componentParameter); interactor.addActiveInstance( component ); interaction.addComponent( component ); return component; }
public Component createComponent(Interaction interaction, Interactor interactor, CvExperimentalRole expRole, CvBiologicalRole bioRole) { Component component = new Component(getInstitution(), interaction, interactor, expRole, bioRole); CvIdentification cvParticipantDetMethod = createCvObject(CvIdentification.class, CvIdentification.PREDETERMINED_MI_REF, CvIdentification.PREDETERMINED); component.getParticipantDetectionMethods().add(cvParticipantDetMethod); CvExperimentalPreparation cvExperimentalPreparation = createCvObject(CvExperimentalPreparation.class, CvExperimentalPreparation.PURIFIED_REF, CvExperimentalPreparation.PURIFIED); component.getExperimentalPreparations().add(cvExperimentalPreparation); ComponentParameter componentParameter = createDeterministicComponentParameter(); component.addParameter(componentParameter); interactor.addActiveInstance( component ); interaction.addComponent( component ); return component; }
Collection<CvExperimentalPreparation> syncedExperimentalPreparations = new ArrayList<CvExperimentalPreparation>(intactObject.getExperimentalPreparations().size()); for (CvExperimentalPreparation experimentalPreparation : intactObject.getExperimentalPreparations()) { syncedExperimentalPreparations.add((CvExperimentalPreparation) cvPersister.syncIfTransient(experimentalPreparation));
if (IntactCore.isInitializedAndDirty(component.getExperimentalPreparations())) { Collection<CvExperimentalPreparation> expPrep = synchronizeCollection( component.getExperimentalPreparations() ); component.getExperimentalPreparations().clear(); component.getExperimentalPreparations().addAll(expPrep);
if (IntactCore.isInitializedAndDirty(component.getExperimentalPreparations())) { Collection<CvExperimentalPreparation> expPrep = synchronizeCollection( component.getExperimentalPreparations() ); component.getExperimentalPreparations().clear(); component.getExperimentalPreparations().addAll(expPrep);
protected void copyComponent( Component source, Component target ) { copyProperty(source, "stoichiometry", target); copyProperty(source, "interaction", target); copyProperty(source, "interactor", target); copyProperty(source, "cvBiologicalRole", target); copyProperty(source, "cvExperimentalRole", target); copyProperty(source, "expressedIn", target); copyCollection( source.getBindingDomains(), target.getBindingDomains() ); for (Feature bindingDomain : target.getBindingDomains()) { bindingDomain.setComponent(target); } copyCollection( source.getExperimentalPreparations(), target.getExperimentalPreparations() ); copyCollection( source.getParticipantDetectionMethods(), target.getParticipantDetectionMethods() ); copyCollection( source.getParameters(), target.getParameters() ); }
protected void copyComponent( Component source, Component target ) { copyProperty(source, "stoichiometry", target); copyProperty(source, "interaction", target); copyProperty(source, "interactor", target); copyProperty(source, "cvBiologicalRole", target); copyProperty(source, "cvExperimentalRole", target); copyProperty(source, "expressedIn", target); copyCollection( source.getBindingDomains(), target.getBindingDomains() ); for (Feature bindingDomain : target.getBindingDomains()) { bindingDomain.setComponent(target); } copyCollection( source.getExperimentalPreparations(), target.getExperimentalPreparations() ); copyCollection( source.getParticipantDetectionMethods(), target.getParticipantDetectionMethods() ); copyCollection( source.getParameters(), target.getParameters() ); }
List<CvExperimentalPreparation> experimentalPreparations = new ArrayList<CvExperimentalPreparation>(component.getExperimentalPreparations()); Collections.sort(experimentalPreparations, new CvObjectComparator());
List<CvExperimentalPreparation> experimentalPreparations = new ArrayList<CvExperimentalPreparation>(component.getExperimentalPreparations()); Collections.sort(experimentalPreparations, new CvObjectComparator());
new CvObjectConverter<CvExperimentalPreparation, ExperimentalPreparation>(institution, CvExperimentalPreparation.class, ExperimentalPreparation.class); CvExperimentalPreparation cvExpPrep = epConverter.psiToIntact(expPrep); component.getExperimentalPreparations().add(cvExpPrep);
if (isCollectionClonable(component.getExperimentalPreparations())) { Collection<CvExperimentalPreparation> expPreps = IntactCore.ensureInitializedExperimentalPreparations(component); clone.getExperimentalPreparations().add(clone(preparation));
if (isCollectionClonable(component.getExperimentalPreparations())) { Collection<CvExperimentalPreparation> expPreps = IntactCore.ensureInitializedExperimentalPreparations(component); clone.getExperimentalPreparations().add(clone(preparation));
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); }
@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); } }
return false; if ( !CollectionUtils.isEqualCollection(getExperimentalPreparations(), component.getExperimentalPreparations()) ) { return false;
return false; if ( !CollectionUtils.isEqualCollection(getExperimentalPreparations(), component.getExperimentalPreparations()) ) { return false;