public boolean testPredicate(Feature targetFeature) {
String targetKey = targetFeature.getKey().getKeyString();
if (sameKey && !targetKey.equals(key)) return false;
Vector<String> chadoNames = null;
if (isDatabaseEntry) {
GFFStreamFeature gffFeature = ((GFFStreamFeature) targetFeature.getEmblFeature());
if (gffFeature.getChadoGene() != null) {
chadoNames = new Vector<String>();
ChadoCanonicalGene chadoGene = gffFeature.getChadoGene();
chadoNames.add(chadoGene.getGeneUniqueName());
List<uk.ac.sanger.artemis.io.Feature> transcripts = chadoGene.getTranscripts();
for (int i = 0; i < transcripts.size(); i++) {
GFFStreamFeature feature = (GFFStreamFeature) transcripts.get(i);
chadoNames.add(GeneUtils.getUniqueName(feature));
}
}
}
String thisFeatureSystematicName = targetFeature.getSystematicName();
for (int i = 0; i < geneNames.length; i++) {
if (geneNames[i].equals(thisFeatureSystematicName)
|| (chadoNames != null && chadoNames.contains(geneNames[i]))) {
geneName = geneNames[i];
return true;
}
}
return false;
}
/**
* @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;
}