/**
* This just returns sf.getBioType() (capitalized) unless its a transcript. For transcript it only
* returns "Transcript" if its part of a Gene. Otherwise it returns its parent's bio type +
* transcript. (should it not tack on the transcript?) Thus a tRNA's transcript would display
* "tRNA transcript", where a gene's transcript would display just "Transcript". Should it
* actually display "Gene transcript"? rename getTypeForDisplay?
*/
public String getBioTypeForDisplay(SeqFeatureI sf) {
String typeDisplay;
if (sf instanceof AnnotatedFeatureI) {
typeDisplay = sf.getTopLevelType();
typeDisplay = capitalize(typeDisplay);
if (!sf.getTopLevelType().equalsIgnoreCase(sf.getFeatureType()))
typeDisplay += " " + capitalize(sf.getFeatureType());
} else {
String db = sf.getDatabase();
// Don't bother showing db name if it is "dummy"
if (db != null && !db.equals("") && !db.equals("dummy"))
typeDisplay = sf.getProgramName() + ":" + sf.getDatabase();
// yet again, the users have requested a change
// Now instead of an enumeration it is the range of the feature
else {
typeDisplay = (sf.getProgramName() + ":" + sf.getStart() + "-" + sf.getEnd());
}
}
return typeDisplay;
}
public boolean keep(SeqFeatureI f) {
FeatureProperty fp = Config.getPropertyScheme().getFeatureProperty(f.getTopLevelType());
return displayType.equalsIgnoreCase(fp.getDisplayType());
}