System.out.println( "\t\tSelect an intact feature, shortlabel=" + intactFeature.getShortLabel() );
System.out.println( "\t\tSelect an intact feature, shortlabel=" + intactFeature.getShortLabel() );
System.out.println( "\t\tSelect an intact feature, shortlabel=" + intactFeature.getShortLabel() );
log.debug("\t\t\tFeatures: "); for (Feature f : c.getBindingDomains()) { log.debug("\t\t\t\tFeature: "+f.getShortLabel());
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; }
log.error("Feature without feature type " + intactObject.getShortLabel()); log.error("Feature without any ranges : " + intactObject.getShortLabel());
log.error("Feature without feature type : " + feature.getShortLabel()); log.error("Feature without any ranges : " + feature.getShortLabel());
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; }