/**
* 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;
}
/**
* Add a new qualifier to a list of qualifiers
*
* @param qualifiers
* @param newQualifier
*/
private void addNewQualifier(QualifierVector qualifiers, Qualifier newQualifier) {
Qualifier qualifier;
if ((qualifier = qualifiers.getQualifierByName(newQualifier.getName())) != null) {
final StringVector newValues = newQualifier.getValues();
final StringVector values = qualifier.getValues();
if (newValues == null) return;
for (int j = 0; j < newValues.size(); j++) {
String newValue = (String) newValues.get(j);
if (!values.contains(newValue)) qualifier.addValue(newValue);
}
} else qualifiers.addElement(newQualifier);
}
/**
* 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;
}
/**
* Read some embl feature qualifiers from a stream into a QualifierVector object. The stream
* should contain qualifiers in this form:
*
* <PRE> /name1=value1/name2="value2"/name3=[value3] </PRE>
*
* @param in_stream the qualifiers are read from this stream
* @exception IOException thrown if there is a problem reading the qualifiers, such as end of
* file.
* @exception QualifierParseException Thrown if the format of the value String is not appropriate
* for a Qualifier with the given name. Each qualifier has a specific format for the value
* part which depends on the name, for example the value part of /codon_start qualifier must
* be a number: 1, 2 or 3.
* @return A Vector containing one Qualifier object for each name/value pair read from the stream.
*/
public static QualifierVector readQualifiers(
final Reader in_stream, final EntryInformation entry_information)
throws QualifierParseException, IOException {
QualifierVector return_vector = new QualifierVector();
BufferedReader buffered_reader = new BufferedReader(in_stream);
String name;
String value;
// loop until end of file
while ((name = StreamQualifier.readName(buffered_reader)) != null) {
// save one character in case the next char is not a '='
buffered_reader.mark(1);
final int next_char = buffered_reader.read();
if (next_char == -1) value = null;
else {
if (next_char == '=') value = StreamQualifier.readValue(buffered_reader);
else {
// this qualifier doesn't have a value
value = null;
buffered_reader.reset();
}
}
final Qualifier new_qualifier;
if (value == null) new_qualifier = new Qualifier(name);
else {
new_qualifier = StreamQualifier.makeStreamQualifier(name, value, entry_information);
}
return_vector.addQualifierValues(new_qualifier);
}
return return_vector;
}
/**
* Change the name of a qualifier
*
* @param qualifiers
* @param oldName
* @param newName
*/
private void changeQualifierName(
QualifierVector qualifiers, final String oldName, final String newName) {
QualifierVector tmpQualifiers = new QualifierVector();
for (int i = 0; i < qualifiers.size(); i++) {
Qualifier qualifier = (Qualifier) qualifiers.elementAt(i);
if (!qualifier.getName().equals(oldName)) {
tmpQualifiers.addElement(qualifier);
continue;
}
Qualifier newQualifier = new Qualifier(newName, qualifier.getValues());
tmpQualifiers.addQualifierValues(newQualifier);
}
qualifiers.removeAllElements();
for (int i = 0; i < tmpQualifiers.size(); i++)
qualifiers.addElement(tmpQualifiers.elementAt(i));
}
/**
* Routine to combine transcript qualifiers and for multiple transcripts create links to the other
* transcripts (other_transcript) and to use the transcript ID.
*
* @param qualifiers
* @param transcript
* @param ntranscripts
* @param chadoGene
*/
private int handleTranscripts(
QualifierVector qualifiers,
Feature transcript,
int ntranscripts,
ChadoCanonicalGene chadoGene) {
QualifierVector transcriptQualifiers = transcript.getQualifiers().copy();
combineQualifiers(qualifiers, transcriptQualifiers, false);
ntranscripts = chadoGene.getTranscripts().size();
if (ntranscripts > 1) {
addNewQualifier(qualifiers, transcriptQualifiers.getQualifierByName("ID"));
List<Feature> transcripts = chadoGene.getTranscripts();
for (int i = 0; i < ntranscripts; i++) {
Feature thisTranscript = (Feature) transcripts.get(i);
String thisTranscriptName = GeneUtils.getUniqueName(thisTranscript);
if (!thisTranscriptName.equals(GeneUtils.getUniqueName(transcript))) {
Qualifier qualifier = new Qualifier("other_transcript", thisTranscriptName);
addNewQualifier(qualifiers, qualifier);
}
}
}
return ntranscripts;
}
/**
* Change the stop_codon_redefined_as_selenocysteine SO qualifier to the transl_except EMBL
* qualifier.
*
* @param qualifiers
* @param feature
*/
private void handleSelenocysteine(QualifierVector qualifiers, Feature feature) {
if (!feature.getKey().getKeyString().equals(DatabaseDocument.EXONMODEL)) return;
qualifiers.removeQualifierByName("stop_codon_redefined_as_selenocysteine");
uk.ac.sanger.artemis.Feature f = ((uk.ac.sanger.artemis.Feature) feature.getUserData());
int translatedBasePosion = 0;
String aa = f.getTranslation().toString();
for (int i = 0; i < aa.length(); i++) {
if (AminoAcidSequence.isStopCodon(aa.charAt(i))) {
translatedBasePosion = i * 3;
break;
}
}
FeatureSegmentVector segments = f.getSegments();
int nbases = 0;
int sequenceloc = 0;
for (int i = 0; i < segments.size(); i++) {
int seglen = segments.elementAt(i).getBases().length();
if (nbases + seglen > translatedBasePosion) {
Bases bases = f.getStrand().getBases();
sequenceloc =
segments.elementAt(i).getStart().getPosition() + (translatedBasePosion - nbases);
if (!f.isForwardFeature()) sequenceloc = bases.getComplementPosition(sequenceloc);
}
nbases += seglen;
}
String pos = "";
if (f.isForwardFeature()) pos = sequenceloc + ".." + (sequenceloc + 2);
else pos = "complement(" + (sequenceloc - 2) + ".." + sequenceloc + ")";
qualifiers.add(new Qualifier("transl_except", "(pos:" + pos + ",aa:Sec)"));
}
/**
* Merge qualifiers
*
* @param qualifiers
* @param newQualifiers
*/
private void combineQualifiers(
final QualifierVector qualifiers, final QualifierVector newQualifiers, final boolean isGene) {
for (int i = 0; i < newQualifiers.size(); i++) {
Qualifier newQualifier = (Qualifier) newQualifiers.get(i);
if (newQualifier.getName().equals("ID") && !isGene) {
continue;
}
// convert GO evidence to codes (e.g. ND=No biological Data available)
if (newQualifier.getName().equals("GO")) {
final StringVector newValues = newQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
for (int j = 0; j < newValues.size(); j++) {
String val = GoBox.getEvidenceCodeGoTextFromText((String) newValues.get(j));
tmpNewValues.add(val);
}
newQualifier = new Qualifier("GO", tmpNewValues);
}
if (newQualifier.getName().equals("product")) {
final StringVector newValues = newQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
for (int j = 0; j < newValues.size(); j++) {
String val = (String) newValues.get(j);
int ind = 0;
if ((ind = val.indexOf(";db_xref=")) > -1) val = val.substring(0, ind);
if ((ind = val.indexOf(";evidence=")) > -1) val = val.substring(0, ind);
if (val.startsWith("term=")) val = val.substring(5, val.length());
if (val.endsWith(";")) val = val.substring(0, val.length() - 1);
tmpNewValues.add(val);
}
newQualifier = new Qualifier("product", tmpNewValues);
}
if (newQualifier.getName().equals("orthologous_to")
|| newQualifier.getName().equals("paralogous_to")) {
final StringVector newValues = newQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
for (int j = 0; j < newValues.size(); j++) {
if (!newValues.get(j).equals("")) tmpNewValues.add(newValues.get(j));
}
if (tmpNewValues.size() == 0) continue;
Pattern p = Pattern.compile("\\w+:link=\\w+");
for (int j = 0; j < tmpNewValues.size(); j++) {
String valueStr = (String) tmpNewValues.get(j);
String newValueStr;
int indexEnd = valueStr.indexOf(';');
String endStr = "";
if (indexEnd > -1) endStr = valueStr.substring(indexEnd);
Matcher m = p.matcher(valueStr);
while (m.find()) {
int index = valueStr.indexOf("link=", m.start());
newValueStr =
valueStr.substring(m.start(), index)
+ valueStr.substring(index + 5, m.end())
+ endStr;
if (newQualifier.getName().equals("orthologous_to"))
newQualifier = new Qualifier("orthologous_to", newValueStr);
else newQualifier = new Qualifier("paralogous_to", newValueStr);
qualifiers.addElement(newQualifier);
}
}
continue;
}
addNewQualifier(qualifiers, newQualifier);
}
}
/**
* 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();
}
}
