@Deprecated @Transient public Collection<Feature> getBindingDomains() { return getFeatures(); }
@Deprecated @Transient public Collection<Feature> getBindingDomains() { return getFeatures(); }
protected void indexfeatures(SolrInputDocument doc) { for (Feature f : component.getFeatures()){ if (f.getCvFeatureType() != null){ enricher.enrichFeatureType(f.getCvFeatureType(), doc); } } } } // End TreeNode Class
/** * @param protein : the protein to check * @return a set of the protein feature ranges which are overlapping or out of bound */ public static Set<Range> getBadRanges(Protein protein) { Collection<Component> components = protein.getActiveInstances(); Set<Range> badRanges = new HashSet<Range>(); for (Component component : components) { Collection<Feature> features = component.getFeatures(); for (Feature feature : features) { Collection<Range> ranges = feature.getRanges(); for (Range range : ranges) { if (isABadRange(range, protein.getSequence())) { badRanges.add(range); } } } } return badRanges; }
/** * Retrieves the features from a participant, initializing them if necessary. * Do not set the initialized collection of features because features cannot be orphan * @param component the component * @return The returned features are ensured to be initialized * @since 2.4.0 */ public static Collection<Feature> ensureInitializedFeatures(Component component) { Collection<Feature> features; if (IntactCore.isInitialized(component.getFeatures())) { features = component.getFeatures(); } else { features = IntactContext.getCurrentInstance().getDaoFactory().getFeatureDao().getByComponentAc(component.getAc()); } return features; }
/** * @param protein : the protein to check * @return a set of the protein feature ranges which are overlapping or out of bound */ public static Set<Range> getBadRanges(Protein protein) { Collection<Component> components = protein.getActiveInstances(); Set<Range> badRanges = new HashSet<Range>(); for (Component component : components) { Collection<Feature> features = component.getFeatures(); for (Feature feature : features) { Collection<Range> ranges = feature.getRanges(); for (Range range : ranges) { if (isABadRange(range, protein.getSequence())) { badRanges.add(range); } } } } return badRanges; }
/** * Retrieves the features from a participant, initializing them if necessary. * Do not set the initialized collection of features because features cannot be orphan * @param component the component * @return The returned features are ensured to be initialized * @since 2.4.0 */ public static Collection<Feature> ensureInitializedFeatures(Component component) { Collection<Feature> features; if (IntactCore.isInitialized(component.getFeatures())) { features = component.getFeatures(); } else { features = IntactContext.getCurrentInstance().getDaoFactory().getFeatureDao().getByComponentAc(component.getAc()); } return features; }
private void synchronizeComponent( Component component, boolean synchronizeAnnotatedAttributes ) { if (IntactCore.isInitializedAndDirty(component.getFeatures())) { Collection<Feature> features = synchronizeCollection(component.getFeatures()); component.getFeatures().clear(); component.getFeatures().addAll(features);
private void synchronizeComponent( Component component, boolean synchronizeAnnotatedAttributes ) { if (IntactCore.isInitializedAndDirty(component.getFeatures())) { Collection<Feature> features = synchronizeCollection(component.getFeatures()); component.getFeatures().clear(); component.getFeatures().addAll(features);
if (!participant.getFeatures().isEmpty()){ Collection<Feature> features = participant.getFeatures();
partIdentMethods = intactObject.getParticipantDetectionMethods(); expPreparations = intactObject.getExperimentalPreparations(); features = intactObject.getFeatures(); confs = intactObject.getConfidences(); params = intactObject.getParameters();
if (isCollectionClonable(component.getFeatures())) { Collection<Feature> features = IntactCore.ensureInitializedFeatures(component);
if (isCollectionClonable(component.getFeatures())) { Collection<Feature> features = IntactCore.ensureInitializedFeatures(component);