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; }