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;
}
protected String getIdForURL(SeqFeatureI f) {
/* 02/06/2004: If user selected a whole result (a FeatureSet),
* neither the id nor the name is what we want.
* So just look at the first child of the FeatureSet
* (which is probably a FeaturePair). Is this bad? --NH */
if (f instanceof FeatureSet) {
f = ((FeatureSet) f).getFeatureAt(0);
}
String id;
if (f instanceof FeaturePair) {
FeaturePair fp = (FeaturePair) f;
SeqFeatureI sbjct = (SeqFeatureI) fp.getHitFeature();
id = sbjct.getName();
if (id.equals("") || id.equals("no_name")) id = f.getName();
// System.out.println("getIdForURL: for feature pair " + f.getName() + ", subject name =
// " + id); // DEL
} else {
id = getDisplayName(f);
// System.out.println("getIdForURL: for feature " + f.getName() + ", display name = " +
// id); // DEL
}
// Special case: BDGP EST IDs look like "LD18592.5prime" rather than "LD18592",
// which isn't what we want. Need to leave out the .[53]prime part.
// (Sima says there aren't any cases where we'd want to preserve that part.)
if (id.endsWith(".3prime") || id.endsWith(".5prime")) {
// System.out.println("Truncating EST/cDNA ID " + id + " to remove .[35]prime");
id = id.substring(0, id.lastIndexOf("."));
}
// Some ESTs IDs have :contig1 at the end
if (id.indexOf(":contig") > 0) {
id = id.substring(0, id.indexOf(":contig"));
// In r4.1, I see EST IDs like UNKNOWN_RE01983:contig1 and INVERTED_GH07123:contig1
if (id.indexOf("_") > 0) id = id.substring(id.indexOf("_") + 1);
}
// Some ESTs have _revcomp at the end, e.g. BE975849_revcomp
if (id.indexOf("_revcomp") > 0) id = id.substring(0, id.indexOf("_revcomp"));
return id;
}