/**
* Handle UTR joins
*
* @param feature
* @param key
* @param qualifiers
* @return
*/
private Location joinUtrs(Feature feature, Key key, QualifierVector qualifiers) {
Location location = feature.getLocation();
if (key.getKeyString().equals("5'UTR") || key.getKeyString().equals("3'UTR")) {
ChadoCanonicalGene gene = ((GFFStreamFeature) feature).getChadoGene();
String utrName = GeneUtils.getUniqueName(feature);
String transcriptName = gene.getTranscriptFromName(utrName);
List<Feature> utrs;
if (key.getKeyString().equals("5'UTR")) utrs = gene.get5UtrOfTranscript(transcriptName);
else utrs = gene.get3UtrOfTranscript(transcriptName);
if (utrs.size() > 1) {
int start = Integer.MAX_VALUE;
RangeVector ranges = new RangeVector();
for (int i = 0; i < utrs.size(); i++) {
Feature utr = utrs.get(i);
Range range = utr.getLocation().getTotalRange();
if (start > range.getStart()) start = range.getStart();
ranges.add(range);
}
if (start != feature.getLocation().getTotalRange().getStart()) return null;
location = new Location(ranges, feature.getLocation().isComplement());
}
int ntranscripts = gene.getTranscripts().size();
if (ntranscripts == 1) transcriptName = gene.getGeneUniqueName();
qualifiers.setQualifier(new Qualifier("locus_tag", transcriptName));
qualifiers.removeQualifierByName("ID");
}
return location;
}
/**
* Maps database (SO) keys to EMBl keys. It will add any extra qualifiers found in the 3rd column
* of DATABASE_MAP_KEYS.
*
* @param key
* @return
*/
private Key map(final Key key, final QualifierVector qualifiers) {
if (DATABASE_MAP_KEYS == null) initDatabaseMappings();
for (int i = 0; i < DATABASE_MAP_KEYS.length; i++) {
if (key.getKeyString().equals(DATABASE_MAP_KEYS[i][0])) {
Key mappedKey = new Key((String) DATABASE_MAP_KEYS[i][1]);
if (DATABASE_MAP_KEYS[i][2] != null) {
Qualifier newQualifier = (Qualifier) DATABASE_MAP_KEYS[i][2];
if (!getEntryInformation().isValidQualifier(mappedKey, newQualifier.getName())) {
try {
final int nvalues;
if (newQualifier.getValues() == null) nvalues = 0;
else nvalues = newQualifier.getValues().size();
final int type;
if (nvalues == 0) type = QualifierInfo.NO_VALUE;
else type = QualifierInfo.QUOTED_TEXT;
getEntryInformation()
.addQualifierInfo(
new QualifierInfo(newQualifier.getName(), type, null, null, false));
} catch (QualifierInfoException e) {
}
}
qualifiers.addQualifierValues(newQualifier);
}
return mappedKey;
}
}
return key;
}
/**
* Maps database (SO) keys to EMBl keys.
*
* @param key
* @return
*/
protected static Key mapKeys(final Key key) {
if (DATABASE_MAP_KEYS == null) initDatabaseMappings();
for (int i = 0; i < DATABASE_MAP_KEYS.length; i++) {
if (key.getKeyString().equals(DATABASE_MAP_KEYS[i][0]))
return new Key((String) DATABASE_MAP_KEYS[i][1]);
}
return key;
}
/**
* Map GFF features to EMBL/Genbank
*
* @param feature
* @return
*/
private Object mapGffToNativeFeature(final Feature feature) {
if (DATABASE_MAP_KEYS == null) initDatabaseMappings();
Key key = feature.getKey();
QualifierVector qualifiers = feature.getQualifiers().copy();
// ignore if obsolete
if (IGNORE_OBSOLETE_FEATURES) {
Qualifier isObsoleteQualifier = qualifiers.getQualifierByName("isObsolete");
if (isObsoleteQualifier != null) {
String value = (String) isObsoleteQualifier.getValues().get(0);
if (Boolean.parseBoolean(value)) return null;
}
}
key = map(key, qualifiers);
if (getEntryInformation().isValidQualifier((String) DATABASE_QUALIFIERS_TO_REMOVE[0])) {
try {
if (this instanceof EmblDocumentEntry)
return new EmblStreamFeature(key, feature.getLocation(), qualifiers);
else return new GenbankStreamFeature(key, feature.getLocation(), qualifiers);
} catch (InvalidRelationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
Location location = joinUtrs(feature, key, qualifiers);
if (location == null) return null;
// flatten gene model - combining qualifiers
if (key.getKeyString().equals(DatabaseDocument.EXONMODEL)) {
ChadoCanonicalGene chadoGene = ((GFFStreamFeature) feature).getChadoGene();
final String name = GeneUtils.getUniqueName(feature);
final String transcriptName = chadoGene.getTranscriptFromName(name);
StringVector sv = new StringVector();
sv.add(transcriptName);
final Feature transcript = chadoGene.containsTranscript(sv);
if (transcript != null && GeneUtils.isNonCodingTranscripts(transcript.getKey())) return null;
qualifiers.removeQualifierByName("ID");
int ntranscripts = 0;
// add transcript & protein qualifiers to CDS
try {
final Feature protein = chadoGene.getProteinOfTranscript(transcriptName);
if (protein != null) combineQualifiers(qualifiers, protein.getQualifiers().copy(), false);
if (transcript != null)
ntranscripts = handleTranscripts(qualifiers, transcript, ntranscripts, chadoGene);
} catch (NullPointerException npe) {
}
// add gene qualifiers to CDS
QualifierVector geneQualifiers = chadoGene.getGene().getQualifiers().copy();
// multiple transcripts
if (ntranscripts > 1 && geneQualifiers.getQualifierByName("ID") != null) {
Qualifier newIDQualifier =
new Qualifier(
"shared_id", (String) geneQualifiers.getQualifierByName("ID").getValues().get(0));
addNewQualifier(qualifiers, newIDQualifier);
geneQualifiers.removeQualifierByName("ID");
}
combineQualifiers(qualifiers, geneQualifiers, true);
} else if (GeneUtils.isNonCodingTranscripts(key)) {
// use gene id for non-coding transcripts
ChadoCanonicalGene chadoGene = ((GFFStreamFeature) feature).getChadoGene();
if (chadoGene != null) {
qualifiers.removeQualifierByName("ID");
QualifierVector geneQualifiers = chadoGene.getGene().getQualifiers().copy();
combineQualifiers(qualifiers, geneQualifiers, true);
}
}
try {
for (int i = 0; i < DATABASE_QUALIFIERS_TO_MAP.length; i++) {
if (!getEntryInformation().isValidQualifier(DATABASE_QUALIFIERS_TO_MAP[i][0])) {
changeQualifierName(
qualifiers, DATABASE_QUALIFIERS_TO_MAP[i][0], DATABASE_QUALIFIERS_TO_MAP[i][1]);
}
}
if (qualifiers.getQualifierByName("stop_codon_redefined_as_selenocysteine") != null) {
handleSelenocysteine(qualifiers, feature);
}
for (int i = 0; i < DATABASE_QUALIFIERS_TO_REMOVE.length; i++) {
if (!getEntryInformation().isValidQualifier((String) DATABASE_QUALIFIERS_TO_REMOVE[i]))
qualifiers.removeQualifierByName((String) DATABASE_QUALIFIERS_TO_REMOVE[i]);
}
if (key.getKeyString().equals("polypeptide")) return null;
else if (key.getKeyString().equals("gene")) return null;
else if (key.getKeyString().equals("centromere")) return null;
else if (key.getKeyString().equals("transcript") || key.getKeyString().equals("mRNA"))
return null;
if (this instanceof EmblDocumentEntry)
return new EmblStreamFeature(key, location, qualifiers);
else return new GenbankStreamFeature(key, location, qualifiers);
} catch (InvalidRelationException e) {
e.printStackTrace();
if (feature instanceof DatabaseStreamFeature) return new EmblStreamFeature();
else return new GenbankStreamFeature();
}
}