/** * @param features * @param qualifiersToTransfer * @param key * @param sameKey * @param isDatabaseEntry * @param geneNames * @return */ private static String[] transfer( final FeatureVector features, final QualifierVector qualifiersToTransfer, final String key, final boolean sameKey, final boolean overwrite, final boolean isDatabaseEntry, String[] geneNames, final StringBuffer genesUpdated) { final TransferFeaturePredicate predicate = new TransferFeaturePredicate(key, sameKey, isDatabaseEntry, geneNames); for (int i = 0; i < features.size(); i++) { Feature thisFeature = features.elementAt(i); if (predicate.testPredicate(thisFeature)) { StringBuffer qualifierBuffer = new StringBuffer(); for (int j = 0; j < qualifiersToTransfer.size(); j++) { Qualifier newQualifier = qualifiersToTransfer.elementAt(j); String qualifierName = newQualifier.getName(); try { if (overwrite) { thisFeature.setQualifier(newQualifier); qualifierBuffer.append( " " + qualifierName + " (overwritten)\n" + parseStringVector(newQualifier.getValues())); } else { final StringVector oldValues; if (thisFeature.getQualifierByName(newQualifier.getName()) == null) oldValues = null; else oldValues = thisFeature.getQualifierByName(newQualifier.getName()).getValues(); final Qualifier newQualifierTmp = getQualifierWithoutDuplicateValues(newQualifier, oldValues); if (newQualifierTmp == null) continue; thisFeature.addQualifierValues(newQualifierTmp); qualifierBuffer.append( " " + qualifierName + " (added)\n" + parseStringVector(newQualifier.getValues())); } } catch (Exception e1) { e1.printStackTrace(); } } geneNames = removeArrayElement(geneNames, predicate.getGeneName()); if (qualifierBuffer.length() > 0) genesUpdated.append( thisFeature.getSystematicName() + " (" + key + ")\n" + qualifierBuffer); } } return geneNames; }