if ( feature.getCvFeatureIdentification() != null ) { CvObject2xmlFactory.getInstance( session ).create( session, element, feature.getCvFeatureIdentification() );
if ( feature.getCvFeatureIdentification() != null ) { CvObject2xmlFactory.getInstance( session ).create( session, element, feature.getCvFeatureIdentification() );
if ( feature.getCvFeatureIdentification() != null ) { CvObject2xmlFactory.getInstance( session ).create( session, element, feature.getCvFeatureIdentification() );
if ( feature.getCvFeatureIdentification() != null ) { CvObject2xmlFactory.getInstance( session ).create( session, element, feature.getCvFeatureIdentification() );
if ( feature.getCvFeatureIdentification() != null ) { CvObject2xmlFactory.getInstance( session ).create( session, element, feature.getCvFeatureIdentification() );
if ( feature.getCvFeatureIdentification() != null ) { CvObject2xmlFactory.getInstance( session ).create( session, element, feature.getCvFeatureIdentification() );
if ( feature.getCvFeatureIdentification() != null ) { CvObject2xmlI cv = CvObject2xmlFactory.getInstance( session ); featureDetectionElement = cv.create( session, element, feature.getCvFeatureIdentification() );
if ( feature.getCvFeatureIdentification() != null ) { CvObject2xmlI cv = CvObject2xmlFactory.getInstance( session ); featureDetectionElement = cv.create( session, element, feature.getCvFeatureIdentification() );
if ( feature.getCvFeatureIdentification() != null ) { CvObject2xmlI cv = CvObject2xmlFactory.getInstance( session ); featureDetectionElement = cv.create( session, element, feature.getCvFeatureIdentification() );
protected void traverseFeature(Feature feature, IntactVisitor ... visitors) { if (feature == null) return; for (IntactVisitor visitor : visitors) { visitor.visitFeature(feature); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(feature)) { return; } traverse(feature.getCvFeatureType(), visitors); traverse(feature.getCvFeatureIdentification(), visitors); for (Range range : feature.getRanges()) { traverse(range, visitors); } }
protected void traverseFeature(Feature feature, IntactVisitor ... visitors) { if (feature == null) return; for (IntactVisitor visitor : visitors) { visitor.visitFeature(feature); } // check if this element has been traversed already, to avoid cyclic recursion if (recursionChecker.isAlreadyTraversed(feature)) { return; } traverse(feature.getCvFeatureType(), visitors); traverse(feature.getCvFeatureIdentification(), visitors); for (Range range : feature.getRanges()) { traverse(range, visitors); } }
protected UniquenessStringBuilder createUniquenessString(Feature feature) { if (keyExists(feature)) { UniquenessStringBuilder builder = getKey(feature); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(feature)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(feature, sb); if (feature == null) return sb; // short label // We need to add the short label for the feature because in mutations in the same amino acid is the only way to // distinguish between two features when the AC is not assigned yet. sb.append(feature.getShortLabel()); // feature type sb.append(createUniquenessString(feature.getCvFeatureType())); // feature identification sb.append(createUniquenessString(feature.getCvFeatureIdentification())); // ranges List<Range> ranges = new ArrayList<Range>(feature.getRanges()); Collections.sort(ranges, new RangeComparator()); for (Range range : ranges) { sb.append(createUniquenessString(range)); } return sb; }
protected UniquenessStringBuilder createUniquenessString(Feature feature) { if (keyExists(feature)) { UniquenessStringBuilder builder = getKey(feature); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(feature)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(feature, sb); if (feature == null) return sb; // short label // We need to add the short label for the feature because in mutations in the same amino acid is the only way to // distinguish between two features when the AC is not assigned yet. sb.append(feature.getShortLabel()); // feature type sb.append(createUniquenessString(feature.getCvFeatureType())); // feature identification sb.append(createUniquenessString(feature.getCvFeatureIdentification())); // ranges List<Range> ranges = new ArrayList<Range>(feature.getRanges()); Collections.sort(ranges, new RangeComparator()); for (Range range : ranges) { sb.append(createUniquenessString(range)); } return sb; }
PsiConverterUtils.populateAttributes(intactObject, psiFeature, annotationConverter); if (intactObject.getCvFeatureIdentification()!= null) { FeatureDetectionMethod featureMethod = featureDetMethodConverter.intactToPsi(intactObject.getCvFeatureIdentification()); psiFeature.setFeatureDetectionMethod(featureMethod);
@Override protected void saveOrUpdateAttributes(Feature intactObject) throws PersisterException { super.saveOrUpdateAttributes(intactObject); ComponentPersister.getInstance().saveOrUpdate(intactObject.getComponent()); CvObjectPersister cvObjectPersister = CvObjectPersister.getInstance(); if (intactObject.getCvFeatureIdentification() != null) { cvObjectPersister.saveOrUpdate(intactObject.getCvFeatureIdentification()); } if (intactObject.getCvFeatureType() != null) { cvObjectPersister.saveOrUpdate(intactObject.getCvFeatureType()); } for (Range range : intactObject.getRanges()) { if ( range.getFromCvFuzzyType() != null ) { cvObjectPersister.saveOrUpdate(range.getFromCvFuzzyType()); } if ( range.getToCvFuzzyType() != null ) { cvObjectPersister.saveOrUpdate(range.getToCvFuzzyType()); } } }
private void synchronizeFeature( Feature feature, boolean synchronizeAnnotatedAttributes ) { feature.setBoundDomain( synchronize( feature.getBoundDomain() ) ); feature.setComponent( synchronize( feature.getComponent() ) ); feature.setCvFeatureIdentification( synchronize( feature.getCvFeatureIdentification() ) ); feature.setCvFeatureType( synchronize( feature.getCvFeatureType() ) ); // cannot call setRanges in interaction because of orphan relationship limitation if (IntactCore.isInitializedAndDirty(feature.getRanges())){ Collection<Range> ranges = synchronizeRanges(feature.getRanges(), feature); feature.getRanges().clear(); feature.getRanges().addAll(ranges); } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( feature ); } }
private void synchronizeFeature( Feature feature, boolean synchronizeAnnotatedAttributes ) { feature.setBoundDomain( synchronize( feature.getBoundDomain() ) ); feature.setComponent( synchronize( feature.getComponent() ) ); feature.setCvFeatureIdentification( synchronize( feature.getCvFeatureIdentification() ) ); feature.setCvFeatureType( synchronize( feature.getCvFeatureType() ) ); // cannot call setRanges in interaction because of orphan relationship limitation if (IntactCore.isInitializedAndDirty(feature.getRanges())){ Collection<Range> ranges = synchronizeRanges(feature.getRanges(), feature); feature.getRanges().clear(); feature.getRanges().addAll(ranges); } if (synchronizeAnnotatedAttributes){ synchronizeAnnotatedObjectCommons( feature ); } }
if (intactObject.getCvFeatureIdentification() != null) { CvFeatureIdentification syncedFeatureDetMethod = (CvFeatureIdentification) cvObjectPersister.syncIfTransient(intactObject.getCvFeatureIdentification()); intactObject.setCvFeatureIdentification(syncedFeatureDetMethod);
public Feature cloneFeature(Feature feature) throws IntactClonerException { if (feature == null) return null; Feature clone = new Feature(); clonerManager.addClone(feature, clone); clone.setOwner(clone(feature.getOwner())); clone.setShortLabel(feature.getShortLabel()); clone.setCvFeatureType(clone(feature.getCvFeatureType())); clone.setCvFeatureIdentification(clone(feature.getCvFeatureIdentification())); if (isCollectionClonable(feature.getRanges())) { Collection<Range> ranges = IntactCore.ensureInitializedRanges(feature); for (Range range : ranges) { clone.addRange(clone(range)); } } clone.setComponent(clone(feature.getComponent())); return clone; }
public Feature cloneFeature(Feature feature) throws IntactClonerException { if (feature == null) return null; Feature clone = new Feature(); clonerManager.addClone(feature, clone); clone.setOwner(clone(feature.getOwner())); clone.setShortLabel(feature.getShortLabel()); clone.setCvFeatureType(clone(feature.getCvFeatureType())); clone.setCvFeatureIdentification(clone(feature.getCvFeatureIdentification())); if (isCollectionClonable(feature.getRanges())) { Collection<Range> ranges = IntactCore.ensureInitializedRanges(feature); for (Range range : ranges) { clone.addRange(clone(range)); } } clone.setComponent(clone(feature.getComponent())); return clone; }