/** * Retrieves the parameters from a participant, initializing them if necessary. * Do not set the initialized collection of parameters because parameters cannot be orphan * @param component the component * @return The returned parameters are ensured to be initialized * @since 2.4.0 */ public static Collection<ComponentParameter> ensureInitializedComponentParameters(Component component) { Collection<ComponentParameter> parameters; if (IntactCore.isInitialized(component.getParameters())) { parameters = component.getParameters(); } else { parameters = IntactContext.getCurrentInstance().getDaoFactory().getComponentParameterDao().getByComponentAc(component.getAc()); } return parameters; }
/** * Retrieves the parameters from a participant, initializing them if necessary. * Do not set the initialized collection of parameters because parameters cannot be orphan * @param component the component * @return The returned parameters are ensured to be initialized * @since 2.4.0 */ public static Collection<ComponentParameter> ensureInitializedComponentParameters(Component component) { Collection<ComponentParameter> parameters; if (IntactCore.isInitialized(component.getParameters())) { parameters = component.getParameters(); } else { parameters = IntactContext.getCurrentInstance().getDaoFactory().getComponentParameterDao().getByComponentAc(component.getAc()); } return parameters; }
if (IntactCore.isInitializedAndDirty(component.getParameters())) { Collection<ComponentParameter> componentParameters = synchronizeComponentParameters(component.getParameters(), component); component.getParameters().clear(); component.getParameters().addAll(componentParameters);
if (IntactCore.isInitializedAndDirty(component.getParameters())) { Collection<ComponentParameter> componentParameters = synchronizeComponentParameters(component.getParameters(), component); component.getParameters().clear(); component.getParameters().addAll(componentParameters);
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() ); }
return IntactCore.isInitialized(((Component) parent).getBindingDomains()); } else if (parent instanceof Component && child instanceof ComponentParameter) { return IntactCore.isInitialized(((Component) parent).getParameters()); } else if (parent instanceof Feature && child instanceof Range) { return IntactCore.isInitialized(((Feature) parent).getRanges());
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() ); }
return IntactCore.isInitialized(((Component) parent).getBindingDomains()); } else if (parent instanceof Component && child instanceof ComponentParameter) { return IntactCore.isInitialized(((Component) parent).getParameters()); } else if (parent instanceof Feature && child instanceof Range) { return IntactCore.isInitialized(((Feature) parent).getRanges());
features = intactObject.getFeatures(); confs = intactObject.getConfidences(); params = intactObject.getParameters();
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 (isCollectionClonable(component.getParameters())) { Collection<ComponentParameter> parameters = IntactCore.ensureInitializedComponentParameters(component);
return false; if ( !CollectionUtils.isEqualCollection(getParameters(), component.getParameters()) ) { return false;
return false; if ( !CollectionUtils.isEqualCollection(getParameters(), component.getParameters()) ) { return false;
clone.setExpressedIn(clone(component.getExpressedIn())); if (isCollectionClonable(component.getParameters())) { Collection<ComponentParameter> parameters = IntactCore.ensureInitializedComponentParameters(component);