private String getDisplayName(SeqFeatureI sf) {
String display_name = "";
// Annot
if (sf instanceof AnnotatedFeatureI) {
display_name = sf.getName();
}
// Not Annot
else {
// FeatPair
FeatureSetI fset =
(sf.canHaveChildren() ? (FeatureSetI) sf : (FeatureSetI) sf.getRefFeature());
// cant do as seqfeature as getHitSequence() is in FeatureSet and not
// SeqFeature and furthermore cant do a getHitFeature().getRefSequence()
// as FeatureSet has no hit feature yet it has hit sequence
// SeqFeatureI fset = sf.canHaveChildren() ? sf : sf.getRefFeature();
SequenceI seq = (fset != null ? fset.getHitSequence() : null);
SeqFeatureI featPair = null; // FeaturePairI fp;
if (fset != null && fset.size() > 0 && (fset.getFeatureAt(0).hasHitFeature())) {
featPair = fset.getFeatureAt(0);
} else if (sf.hasHitFeature()) {
featPair = sf; // fp = (FeaturePairI) sf;
} // else {//fp = null; } // not necasary - already null
if (seq == null && featPair != null) seq = featPair.getHitFeature().getRefSequence();
if (seq == null) seq = sf.getFeatureSequence();
if (seq != null) {
display_name = seq.getName() != null ? seq.getName() : "";
} else if (featPair != null) {
SeqFeatureI hit = featPair.getHitFeature();
display_name = hit.getName() != null ? hit.getName() : "";
}
/* NOT FeaturePair
this will only be reached if not an annot, not a FS w fps
and not a FeaturePair (or if fp hit name is "")
in otherwords a seqfeature result
added getName in for chado gene predics which are leaf seq feats
*/
// shouldnt we check getName != null before using biotype??
else display_name = getBioTypeForDisplay(sf);
}
return display_name;
}
public CurationSet getCurationSet() throws apollo.dataadapter.ApolloAdapterException {
GbrowseAdapterGUI gui = (GbrowseAdapterGUI) getUI(ApolloDataAdapterI.OP_READ_DATA);
String chr = gui.getSelectedChr();
int chrstart = Integer.parseInt(gui.getSelectedStart());
int chrend = Integer.parseInt(gui.getSelectedEnd());
mysql = new MySQLInstance(host, user, pass, port);
db = mysql.fetchDatabaseByName(dbname);
dba = new DBAdaptor(db);
FeatureAdaptor fa = dba.getFeatureAdaptor();
FeatureSetI f = fa.fetchByReferenceStartEnd(chr, chrstart, chrend);
super.clearOldData();
CurationSet curationSet = new CurationSet();
curationSet.setChromosome(chr);
curationSet.setLow(chrstart);
curationSet.setHigh(chrend);
curationSet.setStrand(0);
StrandedFeatureSet sfset = new StrandedFeatureSet(new FeatureSet(), new FeatureSet());
for (int i = 0; i < f.size(); i++) {
SeqFeatureI sf = f.getFeatureAt(i);
sfset.addFeature(sf);
}
curationSet.setResults(sfset);
curationSet.setAnnots(new StrandedFeatureSet(new FeatureSet(), new FeatureSet()));
curationSet.setName(chr + "." + chrstart + "-" + chrend);
// super.notifyLoadingDone();
return curationSet;
}