Ejemplo n.º 1
0
 /**
  * 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());
 }